Be advised that WordPress 2.9 MU is no longer a separate project from the main WordPress branch. It is continuing development as part of the main WordPress 3 branch under the name ‘multi-site’ or MS. This means that you can get all the benefits of both WordPress and WordPress MU versions by using the latest WordPress version. To help you in the process of creating a multi-user website with the latest WordPress version we have created a detailed step by step WordPress multi-site tutorial available here.
One difference between the MU and the standard version of WordPress is that after a theme is uploaded it should be also allowed by the administrator in order to be visible by the other registered members. You can upload your WordPress theme by upload it under your hosting account /wp-content/themes/ directory. You can upload your theme folder via your favorite FTP client. As soon as your theme is uploaded it should be visible under your WordPress admin panel -> Appearance tab.
If you would like this theme to be available for all of your blogs and users in their appearance tab you should allow it via the Site Admin -> Themes
If you would like to start your WordPress MU Blog in a few clicks, check the WordPress MU Hosting package.