In the multisite backend dashboaord, in the top left corner, you have a My Sites link. Hover your mouse over it, and a dropdown will come up. The first option is Network Admin; click on it.
Once you are at the Network Admin section, you can manage your themes and sites.
You can add new themes and list all existing theme.
Note that if you click on Installed Themes, you will also have an option to Network Enable a theme for all sites.
In your case, I would NOT enable any theme for all sites. I would leave the theme disabled, then I would click on Sites, and you will see all your sites listed.
For each site, go to the Theme tab, enable the specific theme for that particular site.
Once you do so, you will be able to restrict the theme to the site.
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