Based on the information provided by one of our customers, here it is the procedure he has communicated to us concerning the configuration of lighthttpd.conf.
The information provided below was not checked and is provided AS IS in hope this will help other customers

 1.- Enabled mod_simple_vhost en your /etc/lighttpd/lighttpd.conf

server.modules  = (
                                "mod_alias",
                                "mod_access",
                                "mod_fastcgi",
                                "mod_simple_vhost",
                                "mod_accesslog" )
2.- Configure a Virtual Host for your Parent Site
     $HTTP["host"]=~ "joomla.puebla.gob.mx"{
                                 server.document-root = "/var/www/lighttpd/puebla"
      }

3.- Configure your Slave Sites using vhost sintaxys for the same Document root
     $HTTP["host"]=~ "joomla.sep.puebla.gob.mx"{
        simple-vhost.server-root = "/var/www/lighttpd"
        simple-vhost.document-root = "puebla"
      }
4.- Restart lighttpd "/etd/init.d/lighttpd restart"

When using Joomla Multi Sites on a Windows Platform, it is required that all the domain and sub-domain share the same directory path.

When you define the domain or sub-domain, you must be checked the permission of the directory that you have create allow to be accessible via Internet. For that, the security permission must include the user "Internet Guest Account".

The second element is to share the same directory path than the master website.

For that, in IIS, when you have a look in the property of the domain or sub-domain that you have defined, you have to check the "home directory".
The local path must have a value identical to the one of your master website.
This is the path that JMS display you when you create a new slave site.

You may also have to check the permission of the domain or sub-domain to ensure that you allow to execute PHP script.
Otherwise, only HTML files can be displayed by your domain or sub-domain.

The following procedure is a summary of the full procedure described by one of our customer and present in the PDF "How to configure JMS with IX Web Hosting". This ful document contain screenshot that can be helpfull.

In summary the operation consist to setup a domain as usual in IX WebHosting and retreive the "HTML Directory Name" that must be used by JMS in the deploy diirectory field. This assume that Symbolic Links is allowed in JMS.

• Login in IX Web Hosting
• Select Hosting Products menu / Manage 
• Click on "Domains" present in the section "Main"
• Click on "Add a new domain" button in bottom right
• Enter the domain name
• When done, edit the domain that you have just created to retreive the "HTML Directory Name" that must be used in JMS deploy directory
• Return in "main" section and select "Web Options" to setup your domain to recognize index.php by default
• Enable MultiViews
• Go now in "Tools" section and start "File Manager"
• Remove or rename the index.html

The present GoDaddy domain configuration is based on the configuration of a customer.

Thsi procedure shows you how to configure several domain to share the same directory path than the master domain.

The steps described below are:

• Login to the "Hosting Management" -> "My Hosting Account"
• Manage the Hosting: Select "My Products" menu, option "Hosting"and in "Control Panel" click on the link "Manage Account"
• Go in the "Domain Management".
  - Open the "Setting" panel;
  - Click on icon "Domain Management" to display the list of domain that are currently attached to your account.
• Clik on button "Add Domain" (top right)
• Enter your "domain name" and specify its "folder".
  For Joomla Mulii Sites, put here the same folder than the one used by your master domain.

Login

Manage account

Domain Management

 Add Domain

 Domain name and folder definition

Here below, we present how to configure a domain or a sub-domain on DreamHost web hosting.
The ScreenShots have been provided by a customers that use Joomla Multi Sites.

In summary, the operation consists in:

• Go in "Manage Domain" and click on "Add New Domain / Sub-Domain)
• When you arrive in the "Manage Domains"
  • "Host to domain": Enter the domain or sub-domain you want to host
  • "Specify your web directory": Change the default value by the directory path of your master website.
    For example
    if you have a "domain.com" with directory "/home/username/domain.com".
    When you define a "subdomain.domain.com" must change the path to "/home/username/domain.com".

Here are the screenshots that illustrate this case

Manage Domain

Specify Website Directory

Some customers use Plesk for the administration of their domains.

Most Plesk users know how to create a domain but not necessary how to provide a specific folder for this domain.
In general the users create a domain that has its own folder.

When working on Unix platform, Joomla Multi Sites Version 1.1.x or higher offers you the possibility to deploy a website in a different directory than the master but only if the Symbolic Links is supported by your hosting provider and if you have the permission to create such links between the directories.
In this case, you can specify the directory that is created by Plesk from within Jommla Multi Sites.

If you want to use the same directory as the master website (as we recommend), the procedure below is provided by one of our customers.
We are providing it to help Plesk users in the configuration of their system.
We cannot guarantee the accuracy.

In summary:

• Login into Plesk
• Click on Domain
• Click on the Master domain on which you want to add alias
• Click on "domain alias" 
• Add the different slave sites as an alias domain of your master.
  As the slave sites are defined as an alias (synomym) of the master website, they automatically also use the same path of the master websites. This means that they share the same files and folder of the Joomla Installation.

 Login into plesk

Click on the domain

Click on the "master-domaincom" to enter in the DNS definition of this domain

Click on Add Domain Alias to declare the slave sites as a synonym (alias) of the master website

Joomla Multi Sites (Version 1.0.x and also Version 1.1.x when Symbolic Links is not available) requires that ALL the domains and sub-domains SHARE the same directory (The Joomla Installation - Files and Folders).

The procedure below describes how to check if the Domain Hosting is correctly configured for each of the domains that you want that Joomla Multi Sites manage.

This procedure does NOT require Joomla Multi Sites and can be tested totally independently without anything else than the "hello world" files that you can be download here.

The objective is to install a "hello word" file into the directory of your master domain and check if you can see also this files from the domain that will be used as slave domain.

The hello.zip file contain:

• hello.txt : This file contain "Hello world";
• hello.php : This file is a php script that:
  • display the text "Hello world script";
  • display the current path where it is installed
  • test if the Symbolic Links are available on your environment
    This last point is important when your different domains are located and defined into separated directories.
    In this case, the Symbolic Links could be (conditional) used to create a bridge between the master directory and the slave directory. Perhaps you will encounter permission problem to create the bridge between the master and slave directory.
  • When the slave sites is located into another directory than the master website AND the Symbolic Links is present then this script also allow you to test the creation of the bridge between the Slave Site and the Master Website.
    This allows you to verify if the Joomla Multi Site Symbolic Link feature present in the version 1.1.x can be used.

If you want to see a sample of results of those scripts and therefore the expected results here are some links that you can use.
Master website URL:

• http://master.demo.jms2win.com/hello.txt
• http://master.demo.jms2win.com/hello.php

• http://slave1.demo.jms2win.com/hello.txt
• http://slave1.demo.jms2win.com/hello.php

Notice the both Master and Slave websites display exactly the same "The current path is".
This is because the Domain hosting share the SAME path (share the same joomla installation - share the same files and folders)

"Hello world" Installation and test procedure

• Unzip the hello.zip file into the root of domain you will consider as it will be your master websites.
• Enter the URL http://www.master_domain.com/hello.txt
  You should see the "Hello world" text displayed.
  • If you see the "Hello world" text, you can repeat the operation with the script "hello.php"
    http://www.master_domain.com/hello.php
    This script will display "Hello world script" and additinoal information such as the path where it is installed and if the Symbolic Links are available
• Now that you know the the"hello" files are correctly installed on the master website, you can check the slave site domain hosting configuration
• If the "hello.php" display that "Symbolic Links IS NOT OK", this means that is mandatory to map all the slave sites into the same path than the master website. The path is the one displayed by "hello.php" script.
• If the "hello.php" display that "Symbolic Links is PRESENT", this means that it should be possible to have the slave sites deployed into an external directory. Perhaps you will encounter later problem with permission.

Test that slave sites are mapped in the same directory than the master website

The objectif is to check that you can see the "hello.txt" file from the other slave domain.
To help you, the "hello.php" script display the path that must be used when you setup the slave domain into your Domain Hosting tools.

You can have different scenario:

Case of another domain than the master domain

He this is the case of "www.slave-domain.com" and "www.master-domain.com".
In this case, it is necessary to ensure that both domain (slave and master) use the same full path.

GoDaddy - Domain and Sub-domain setting with the same folder path

This is a summary of the steps to configure GoDaddy:

• Login to the "Hosting Management" -> "My Hosting Account"
• Manage the Hosting: Select "My Products" menu, option "Hosting"and in "Control Panel" click on the link "Manage Account"
• Go in the "Domain Management".
  - Open the "Setting" panel;
  - Click on icon "Domain Management" to display the list of domain that are currently attached to your account.
• Clik on button "Add Domain" (top right)
• Enter your "domain name" and specify its "folder".
  For Joomla Mulii Sites, put here the same folder than the one used by your master domain.

 See also Godaddy Configuration here.

CPanel  - Same path using AddOn Domain

When using CPanel, this can be achieved with AddOn domain where you can specify the path that must be used by the domain. Becarefull if you are using different CPanel account. In this case, it is probable that path will be different as they will be relative to each account. You probably will have to consider using Symbolic Links to create a link between the different accounts.
In summary:

• Go in CPanel and select AddOn domain
• Once in the AddOn Domains, then you will see an interface similar to this:
  Create an AddOn domain
  • New domain: the “slave site” name
  • Document Root: This is the root where the Master Site with the installed component is installed.
    This is also the path that is displayed by JMS after it has created the slave site (see the message in blue in the top)

See also CPanel Configuration here. For screen shot provided by one of our customer: click here

When you have configured your CPanel, you can test the "hello.txt" file and "hello.php" scripts.

Plesk - Create an alias domain on the master domain
When using Plesk tool to configure the Hosting Domains, this can be achieved in defining domain alias on the master domain.
When you define an alias, this automatically use the same path than your master domain as it is defined as a synonym (an alias).
The procedure conisists in:

• Login into Plesk
• Click on Domain
• Click on the master domain to manage it
• Click on "alias domain" to create alias on the master domain
• Create entries for the slaves domain.

To have a more detailled description of this procedure and screen shot, see How to configure Plesk alias domain.

Case of sub-domains using the same domain than the master domain

He this is the case of "slave1.master-domain.com".
In this case, you can generally defined the sub-domain (slave1) as a Hosting Domain alias of your (master-domain.com).
When you define an alias, this automatically use the same path than your master domain as it is defined as a synonym (an alias).

Joomla Multi Sites requires that all the websites (master websites and all the slave sites) share the same Joomla Installation folder.

This mean that you have to setup each domain to be mapped on the same folder.

In the procedure below, we summarize the different steps to folllow.
We also provide you a link to a document provided by one of our customer that explain with screen shot, the different steps he followed to configure CPanel.

In summary:

• Go in CPanel and select AddOn domain
• Once in the AddOn Domains, then you will see an interface similar to this:
  Create an AddOn domain
  • New domain: the “slave site” name
  • Document Root: This is the root where the Master Site with the installed component is installed.
    This is also the path that is displayed by JMS after it has created the slave site (see the message in blue in the top)