I always test fit fuselage seams. If you know there is a mis-match, you can do some things that are too late to do after the halves are joined. If one side is wider than the other, sometimes making a couple of "formers" to draw the width in a bit may save some filling. Sometimes you can fit up clamp supports to clamp and squeeze the wider side.
For any residual mismatch, I like to try working with both sides, filing and sanding the wider side and putty on the narrower side.
Sometimes the problem is not unequal widths, but an offset due to locator pins not being in exactly the right spot. Two possible fixes for that. First, try enlarging the holes/dimples on the female side. If that is still not enough, cut the locating pins off completely, like many of the European kits. Makes gluing things together a little harder, but pays off in less seam filling.