Beta testing – can you use multiple subdirectories

This is my first time to use WPMU. I’ve got a dedicated server and I THINK I would like to set up multiple directories such as /CMS1/, /CMS2/, etc. and upload a separate installation of WPMU to each directory for beta testing. In theory, I would then use a different theme in each version so I could just switch folders and compare how they look and function. Would this work?

Also, if it does work for beta testing and I find I like /CMS2/ and I want to make it live, can I do it with a simple redirect index.html on the main domain? If not, and I need to move it to the root, are the permalinks or anything else going to be messed up because of the move?