So far as I am aware, the FL rendering engine doesn't support bump-mapping of any kind. It supports simple and alpha-channel transparency, simple and alpha-channel lightmaps... and that's it. FL's textures look like they're bump-mapped, but they just faked it- it's pretty easy to do
Now, before you panic... I have thought of a way to save your work, at least for the most part!
What you can do... is take your uvmap and bumpmap (I am assuming that you've made both as a single, seamless map, not a tilemap... but it'll work for tiles, too) and put them onto a plane or a cube (depends on what kind of renderer you're usually used to working with, of course). Then put a light into the scene and put it at a 45-degree angle or so... and render a non-perspective view of the face/plane. The light will give the bumpmap the proper amount of lighting and shadow, and it'll look mainly right when you apply the combined file to your ship. Just be careful about the light's position and trajectory, so that any specularity is from the bumps. This final render, after being cropped and positioned correctly in Photoshop, will serve as your final texture- with the desired amount of bumpiness.
My approach to bumps is a little different. I usually make my texture with bumps by layer-manipulation and very gentle touches of light here and there. The key with bumps is that they should be subtle- otherwise they just look unprofessional and tend to make your textures look incoherent.
If you're still lost, and the above all seems like gibberish, I suggest that you download my H-Fuel Tanker, which featured a lot of fake bumps, or download one of Porche's better (more recent) ships, which have pretty good detailing for their resolution.