Correcting BAD seams in constructing Aircraft

Here are two links that should help you out, the first is all about how to deal with that seam problem.
http://www.swannysmodels.com/Seams.html
And this one is all about my construction of the Revell B-17F
http://www.swannysmodels.com/B17Ebuild.html
I did convert it to a E model but the fuselage is mostly the same as the F

You should put tape on the areas around the seam so you don't damage those while sanding.

if it's just a gap, fill it with putty, thick paint, or gap-filling superglue, then sand smooth.

If the parts are uneven (one part is higher than the other) and there is absolutely, positively no way to correct the problem before assembly (i.e. warming and warping the parts, removing alignment pins, adding some styrene or putty) your choices are pretty limited. The best way is to bite the bullet, sand the joint smooth, and rescribe the panel lines with a X-Acto knife. You can use tiny drops of glue to replace the lost rivets.