Sometimes on a WPMU system, you may wish to have a theme enabled just for one blog. The main blog is a good example,. because you do not want users able to choose the exact same layout as the main blog with any custom coding it may have.
First, make sure the theme is not active site-wide. If you have just uploaded the theme, it will be like this by default. If it is already enabled, you just need to go to Site Admin -> Themes and click No, then Update Themes to disable it.
To enable the theme for just one blog, go to Site Admin > Blogs. Find the blog in question and click Edit. This will bring you to a page to edit all variables for this blog, including a list of disabled themes on the far right. This time, there is a checkbox by each disabled theme name. Check the one you’d like to enable for this blog, scroll down, and click the Update Options button.
When the admin of this blogs goes to the presentation page, they should now see the new theme. Other blog admins will not be able to see it in their Presentation menu. You can test this as a site admin by visiting the backend of the blog in question.