umm... well it takes more to texture a ship then just applying a skin to it. You have to assign uv maps to the mesh so as the 3d model knows how to apply the skin to it. There are various programs specifically designed for this, such as lithunwrap, however if your starting out I wouldn't suggest that. Also lithunwrap doesn't keep track of shading groups which is why I only use it for taking screenshots of my uv map to paint over... but I don't think you should be worrying bout those yet either.
In milkshape, select a group or faces of that group which have a material assigned to them, then press ctrl-t or manually click on the texture coordinator under the windows tab. In the scroll box in this window select the group inwhich you have faces selected in the milkshape window. Click region then remap. You should see how it works from that. The various angles in which you can chose effect the direction the remap takes it. For the most part, if you have a plane, you want the angle at which the plane takes up the most volume on your screen to be the angle you remap it as in the texture coordinator.
Just as a suggestion when you use uv mapping in milkshape, it is occasionally hard to select the specific faces of a group you want to remap, so sometime it is best to hide a number of the other faces. Because of how the texture coordinator works if you hide a face in the main window adjunctant to the face your remapping, you can't move the vertex points in the texture coordinator. As a way to get around this before you start texturing. Select your entire model, go to the vertex tab on top, and click unweld. Then Texture coordinate all your panels; then reselect your entire ship and press ctrl-w to re-weld all those faces together.