So I was wondering, how do you rate the version of a game like Beta 3.5, Alpha 6.2, or v8.3.6? Is there a certain order? I think the number that the version goes up every time is the priority of the thing added, but I can't be sure.

Versions are just different versions of the same project, really. :p The higher the number, the newer the version is and the closer the project is to completion. There's no specific order you need to use, you just start at v0 and keep going up. You judge how much the version should go up by each time, but the more you add, the more you go up by, usually.

Would it be better to just keep working on the same project and have it move back as you create more projects, or to just make a new version? Don't tell me the ups and downs (I already know them) , but actually tell me which one works better. Also, how do I change the starting screen (before you click the green flag) ?

It looks like this, with everything behind the green flag darkened:
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