The best way I have found is to use a contour guage. This is a tool that has lots of metal wires that slide back and forth. By pushing the wires against an object you get a very good outline of it. That outline can be transferred to cardstock or plastic.
I tape the fuselage together first. Then mark out the location of the floor, instrument panel and bulkheads. Next I seperate the fuselage and use the contour guage to get the outline of where the bulkhead would be. Make a straight line on the material that you will use for it (I use thin sheet styrene .020 or .030). Place the guage on one side of the line and trace around it with a sharp pencil. Flip it over and trace it again to get the other half of the fuselage. Use scissors to cut it out. Then sand it to its final shape, dryfitting often so as not to remove too much.
Now you can use strip styrene to replicate stiffeners, stringers, brackets and whatever else you need to, good reference materials are key too this part.
You may also sand the kit part flat and use it as a guide to trace out a new one. Sometimes I do this too depending on the situation.
hope this helps
Darren