As promised, here is an example of how I envision the overlays working. [I took the sections I have already mapped and cut them down into overlays. Future overlays will be more original.] I used the Engineering section (see above) as the base map and added the armory, the bacta ward, and crew's quarters.
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Name:	Bacta Ward.jpg 
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The resulting map looks like:
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Name:	Starship Sections - Overlay Example.jpg 
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I can already see some improvements I need to make: 1) scale each overlay so that they can drop on top of the appropriate section; 2) remove the walls from the overlays so that the overlays can be arranged is any order; 3) provide each overlay with the same basic flooring pattern so that it is less obvious what is an overlay and what is part of the original map.

As usual, I am open to any comments or criticisms.

Hoel: I agree that these maps don't demonstrate an efficient use of space. What do you recommend to improve this? Should I close up the hallways more? Should I put more objects on the map? Thanks.