I'd like to see a pic of the problem too. But I would say to strip the paint off before you put the fuselage together, get it back to a clean slate. Then glue the fuse halves together, do all the seam work, mask off all windows and spray again. But then again, are you spraying or brushing? What kind of paint, enamel or acyrylic? How much work is done to the interior?
You can strip off the paint by either soking the fuse halves in simple green for a day. Or spray on oven cleaner, this way your better able to control where the oven cleaner goes.
You've got options depending on what you have done already. And like Daddy1 said, sometimes black as used as an undercoat but that depends on what kind of paint you are using, regular enamels, alclad etc... Plus it depends on if you brush or airbrush.
I need more info, and pics would help.