stindle -
Any seam that isn't there the the real article should really be assembled first filled/sanded or otherwise made to disappear, before you paint. If you paint first, no matter what you do, besides re-painting :D , will allow the seem to show. What I generally do is assemble the sub-assemblies, like ordinance, fill/sand etc and then paint those before attaching them to the main body. Things like wing and fuslage halves deinately go together before painting.
In the case you mentioned, even though the parts are painted, you can do a careful gluing, sand, fill in necesary, and repaint/touch up, or just get a new model and start over, ;).
Archer out.