subdomain mulitsite on localhost in a subfolder

I have a sudomain-based WPMU installation locally with xampp. My vhosts lists domains like follows:

127.0.0.1 mainDomain.com
127.0.0.1 siteA.mainDomain.com
127.0.0.1 siteB.mainDomain.com
127.0.0.1 siteA.com
127.0.0.1 siteB.com

The WordPress MU Domain Mapping PlugIn maps “real-domains” on system-subdomains.

To have a standard project structure, I would like to move my installation from the documentRoot to a subfolder.

My question is, what do I need to do, to accomplish that and will it have any consequences for the compatibility between my local- and a live-system?

Multisite cannot be installed in a subdirectory of the document root currently. This will be possible in 3.5.

See Multisite on Windows with wildcard subdomains for a guide how to manage subdomains automatically on Windows with XAMPP. You can move the plugin directory to another directory per wp-config.php. This is possible for themes too, but automatic theme upgrades will fail currently.