First off, when I export my ship from Sketchup to 3ds and open it with truespace, it separates random spots on the ship into separate meshes. Is this okay? If not, what do I have to do to make it okay?
If you're having problems with things like a chunk of your hull importing into trueSpace as a separate object, leaving a faceless hole in the in the other part of the hull, then you're experiencing geometry problems in Sketchup.
From some of the models I've seen people do with Sketchup, it's apparently easy to inadvertently get edges and vertexes occupying the same coordinates without them being connected.
Think of a pair of playing cards leaned up against one another. They're two separate objects yet their upper edges are practically in the same space. Apply a bit of glue and they're a single object.
I've seen this same problem with just about every format trueSpace can import. trueSpace has always been designed to work with solid models, going all the way back to its early days as an Amiga program. (Thus the funky UI, blame it on Amiga!) Several other 3D programs can take a mess of one-sided polygons with their edges "leaned up against each other" and manipulate the collection of bits flying in formation as if they really are a single object.
How does Freespace handle non-solid meshes? Does it choke on them or will it go ahead and work? If it can't tolerate non-solid meshes, I suspect that's why trueSpace's .cob format was the original format of choice for modders- because you cannot make a non-solid simple object* in trueSpace without deliberately deleting a face.
*Well, in 3.2 and earlier you can, if you distort non-triangles too far you can "rip holes" in the mesh. 4.x and later are much better at handling extremely non-flat polygons with 4 or more sides.