In MU, users do not have access to the server, and the site admin is the one who will upload new themes. They stil go in the Themes directory just like in regular WordPress. Before they will show up sitewide for all users, the admin must enable it.
Go to Site Admin -> Themes. Here you will be presented with a list of themes installed on the server. There is a colum, called “active” with Yes and No radio buttons. New themes are set to No as a default. Click Yes and scroll down to the button called “Update Themes”. Click to save your changes.
Now users will be able to select the theme you’ve just uploaded.
In case you forget this step, a handy message will be displayed to the Site Admin only when they visit the Presentation page. It will show up in light blue at the top as an alert, with a friendly reminder and a link.
It is also good to remember that all theme files are shared by all users. If you make a change to a theme that is enabled for all users, then every blog using that theme will have the same change.