Why not just create limbs at the locations you want in your modeling program and then export it as an .x model? For example, where you want the exhaust from the ship to come out, just place a limb there (connected to the root limb of course) and use the limb position commands to determine where the exhaust port is in 3D space.
I think with .3ds format models, DBP recognizes the individual meshes as limbs, but I also think it goes to the center point of the limbs as to the x, y, z location and would not be as accurate as creating limbs/bones and using an .x format model.
I can further illustrate this if needed, or if you want to send me your model, I can rig it for you to show you what I mean.