I just converted a site to a multisite setup using WordPress 3.0.4. One thing I found in a hurry is that if I wanted to edit a theme's code, the changes would be reflected on all the subsites that use the same theme. Is there a to customize the code so that only a certain subsite receives the changes??
If it is just css customizations, use this plugin: http://wordpress.org/extend/plugins/safecss/
It's what wp.com uses for their css upgrade.
If you have to edit the php, make a copy of the theme with a new name on the theme folder and in style.css.