Whoa, You are getting a little ahead of yourself...Let's go backwards a minute, That putty you are using is for patching oil pan leaks or something, But you got it flat so let's just leave it there and hope for the best, We need to bury that with a glaze putty, At the car store they sell a cheap laquer based stuff in a toothpaste tube, cheap, and shrink, but fine for that...Level it off, lightly sand, permatex rust kill actually acts like a sealer, spray the area, primer would be optimal but in the interest of saving some money, paint the area (just the spots) 3 light coats let dry, lightly sand...And hang it on a wire, frame door open and all, wipe it down with alcohol, and paint it all at once...This way you don't have to tape it off to do it in stages, tape on fresh paint should be avoided, especially with a cheaper, slow drying hammer finish bomber can, since it will leave tape marks...Paint it all at once, no paper, no tape, just really clean and door open so you get everywhere...It is frustrating I know, but once you understand flat and compatible, there ain't much you can't do.