Multiple installation options

I currently have two installations, one in the root dir and one in a subfolder. I now need to add a new installation with a different domain name.

So far I’ve tried putting it in a /vhosts/subdir/ and changing the .htaccess file to point there, which sort of worked, although there are permalink issues and new themes are all greyed out and not functioning (not a plug-in issue – tried that).

My question is, given the two installations I already have, and the new one I need to add, is it best to try to reconfigure everything with the new WordPress 3.0 Network system? Or what? I tried the WP Hive plug-in but it didn’t seem to work – nothing appeared when I clicked Add New.

Any idea how to proceed without breaking what I already have? Thanks.