If I paint a project say yellow and blue and then go over the project with an acrylic antique finish will that mess up the paint?

Yes, it will. If you paint with acrylic paint, and then start wiping acrylic antique on top of it, you’ll definitely disturb the paint. You’ll need to put a good sealer on top of it if you want to do that – several coats.  Probably something acrylic like leather sheen, super sheen, or maybe RTC.