then dont split them between maps. 
hold on...
EDIT:
select the faces that you want to break off in the UVW editor, collapse the stack (convert to editable poly) break off the polys in the geometry that are mapped on the map you want to break off seperate (wich SHOULD be selected for you since you did it in the editor ;) ), apply a uvw unwrap to both and presto. done with map coordinates preserved.
google mate. im POSITIVE theres a modeling tutorial for it.
Already split the Secondary Hull into two maps. The Nacelles, the pylons, and the shuttle "landing strip" (basically the parts of the pylons that wrap around the aft end of the ship) are one map. The rest of the secondary hull (the oval cylinder and neck) is one map. And I've modified the Unwrap (three times) to better use the space available for the deflector dish, shuttlebay doors, impulse manifold, and dorsal spine.
im really loving this ship more and more! cant wait to add her to my install 
one quick question tho - are all the windows going to be lit? or will you have some lit and some unlit? seems having some unlit would be better? just my personal opinion tho...
As of right now, all the windows are remaining lit until the finishing touches on the mesh are made, simply because it's easier for me to keep track of the way the ship looks with them all lit. When I get close to completing the textures, I will go back and add the finishing touches to the windows such as a pattern overlay, and change the color of the windows to a more bluish tint. At that same time, I'll select which windows will be unlit.
BTW, I'm looking for ideas/suggestions for the Aztec pattern on the secondary hull. I want something more unique than what I did with the saucer.
