how to make main multisite site independent of Prosite

I am in the process of setting up Prosites. One thing I noticed is that my main site seems to have picked up some of the restrictions of low level Prosite settings. For example, I had previously set a high upload limit to this main site, but now there is a message in admin area saying to upgrade to get more space.

Does the main site have to be designated a level now that Prosites is active? I did watch the video tutorials, but I don't remember hearing anything about how to handle the main site for a multisite installation.

Thanks, Joe.