Well, you look at the name of the texture you want to replace and the one you want to use, then you put them in their respective textboxes. You don't need to replace -shine,-normal or -glow maps, FS will do that for you. Simple as that.
HOWEVER, not all ships are textured the same way. In the specific example you mentioned, the Leviathan (at least the hi-poly one) has been UVmapped (i.e. the entire ship uses just one texture), while the Raynor has been tilemapped (i.e. uses multiple textures). Try it out, you'll see that the result looks really bad. UVmapped ships usually require a custom-made texture if you want them to look different.
You can, for example, make the Orion or the Colossus use Raynor textures, since both ships are tilemapped; but if you really want a different-looking Leviathan you'll either have to use the retail model (which is tilemapped) or make a new texture for it - in which case you can use texture replacement to make it use the new texture, of course.
