WordPress MU

I have a dynamic domain: url.url.com. I had a wordpress mu setup in the root dir. Now I am working on a second version and I tried to put it in a subfolder.
url.url.com/beta/

I can get the front page to display but all the associated links don't work. Is this a limitation of WP or do I need to setup something different with apache?
Ideally I would like to have both versions in a subfolder.

url.url.com/alpha/
url.url.com/beta/

Thanks

google multisite manager and donnchas domain mapping plugin. that'll be easier than what youre trying to do.