Hi all; so I know that uploading a gedcom will over ride the one you have; but I also have seen mentioned on here, people have multiple files uploaded. Is that only the paid part, or can you do that on the free site?

Create a new tree - go to your account and click on the "Create a new website" link. I have 2 paid for and 2 free trees.

If you pay for an upgrade is that per tree? Let's say I have 3 free trees, would an upgrade only count towards 1 of those free trees?

Yes, if you have 3 free trees and you upgrade No 2 to premium, then it only applies to No 2, Nos 1 & 3 are still free and NOT premium.

Thank you!