You don't. Sins models use a single texture, so you simply have the model UV mapped in such a way which allows you to paint the texture according to specific areas on your ship. In other words, you do not apply separate materials within XSI or other modelling package, you apply a single material with all the textures assigned to it as described in the Forge Tools 3 documentation.
If you don't know how to UV map, well, you gonna have to learn. 
I suggest googling for UV mapping tutorials for the program you use to get yourself started. It may look complicated, but it really isn't once you learn your way around. Its actually more tedious than difficult (UV mapping is my least favourite part of making a model).
