I setup a master site at master.domain.com.This has multisites and other extensions installed in it but no content. Now I want to setup my domain.com I want it to have all the content of the master. I watched the video showing to create a rule but it shows sharing from a new slave to 2 more slaves. I don't have any slaves setup yet so how can I create a rule? Do I need to create a rule if I will not be duplicating this page. It will just be a home page that goes to other pages/ sub domains.

If you want to replicate the master websiste, search in this forum for "replicMaster".
We describe that plenty of times.
See also the tutorial video 0.d and moreless at the middle, you have the replicMaster rule that is shown.

www.jms2win.com/en/forum/24-joomla-multi...ng-a-slave-site#8413

Think of Yahoo, They have a Homepage and when you click on a section it takes you to that subdomain with that sections content. That is what I am trying to do.

Master holds on the programs

Homepage links to other subdomains (sections) also where users register, use jomsocial,etc

when a section is clicked it goes to that subdomain.

So master is master.domain.com
homepage domain.com (slave)

Section is subdomain (slave1)
- sub sections (slave1a)

The homepage will just be used for people to register and use jomsocial. If I replicate the master then homepage will be sharing extensions used by other slaves but wont be needed for the homepage. Example SobiPro. So do I setup the domain.com as a slave or replicate the master?

As you can see in my recommendation, in general, I consider that the master website just content the extension without any content. This is a library or a repository where the extensions are available to build the slave site.

If you want to start replicating the master.domain.com to build the www.domain.com, you can do it or you can also create a fresh slave site where you decide to install parts of the extension present in your master.
All depends if it is faster to uninstall or install something.

Both replication or fresh slave is possible.