RE: Cut before or after painting?
I always paint then cut, as you will get better results that way (if you are going all out with the air brush).
Then for a backing coat I use Rust-Oleum Crystal Clear Enamel as a backer. Also I use it right over water based paints without an issue (just be sure to let the paint cure first). Although I don't know if it will cause an issue or not, I would say yes you can use an enamel paint as a backer/sealer (I'm not sure on that tho, so be carefull if you do, do it).