You can do it the hard way if you like too.
Have the model's default color be rather bright, like a light blue or something, with the default background as black. Now render a HUGE image of each of the 6 main faces of the ship.
Color those in psp or photoshop, however you see fit.
Then select all the faces you want each image to cover and hit spacebar (to lock the selection). Then drag the appropraite side down from the materials list.
You will still have to fight with the tiling and whatnot to make it all fit just right. Such as the image should not have ANY leftover space above or beyond the limits of the ship. (If the ship's image is 300x600, but the rendered image has a border of about 50x50, that useless data will screw with the mapping.)
Hope that made sensel :/