I was having some trouble with templates (the visual design, not the multisite 'template') and when I had sh404SEF, it would not be able to find the correct path to the templates folder.

So here is what I did to fix make it work.

In my templates, for any paths I put



to get the base URL and then follow with the path. I haven't noticed any other problems as of yet with sh404SEF, but someone else mentioned it caused some issues. So if you add this in your paths in your index.php file of the template, it seems to function.

Thank you for your contribution that highlight the fact that some themes (template) may have an implementation that require to have the directory "templates" just below the root of the domain. This may be also the case for the images.

When you deploy a website in {site_dir} and the themes folder in {site_dir}/templates, this allows to keep the directory structure.
Perhaps you also have to specify the media and image folder to have respect this directory structure.
This may solve the problem without having to modify the themes code
Remark: This solution should work for domain and sub-domain but may not be working in the case of sub-directories