Only a relatively few kits are built in that way - mainly the plank-on-frame type. Some can be built flat down on a building board while others are "self-jigging" in that the parts will only fit together in the right way. There should be adequate instructions to show you how to go about building the model. For example, I'm in the process of building a Vintage Model Boats Co 'Police Launch' and this is build up around a ply "box" structure, using tabs and slots to locate and hold the parts onto it before applying the gloop. Redesigning and/or remaking the bulkheads in any kit should be unnecessary (I exclude Dumas kits, but that's another story!).
DaveM