Hi, Dave, thanks for the response!
I’m adding a diagram that will perhaps explain the situation a little better!

So, the two blocks, intro and outro, will never change. They’re represented as they sort-of look. I’ve animated these in After Effects and this animation is of a complex kind that could never be reproduced in Premiere. The green in the background should become transparent, and it does, the problem is that it also takes away the green from the logo! And there’s nothing I can do about the logo. The logo also has blue, so it’s the same issue with using blue in the background (plus, the end result isn’t as good). To be brief, the logo and images from the intro/outro are so colorful there’s no one color that can be used as a background that is not somehow repeated in the foreground.
So what I’m thinking is I could apply Ultra Key and then mask in the green parts I want in Premiere. I can follow them as they move around the screen; this’ll be a tiresome job but I hope I could do this only once and then just preset these modification or something similar. That would also help me with the background music, as I could have it set up so the levels automatically go up and down for the portion where the intro and outro play (the outro would probably have to be done manually, which is no problem; but at least the intro could be automated, I think).
I could set these block as a separate importable project (can this be done, like in AE?) but it seems like an impractical workaround, and that Pr should have a way of doing this. Otherwise (and I realize this is a question for the AE forum) is there a way to get this animated footage from AE to Pr without the background?
Thanks again!