Turns out they're not that large, after all. I'll upload a couple for public scrutiny. Not fancy, but highly functional.
The superimposed grid is, I think, 1cm x 1cm. It worked great for unit counters, and probably would be fine for miniatures. I printed them onto cardstock, which was plenty thick -- didn't feel flimsy like plain paper would've.
Each unit has a unique letter, A through Z (with a few missing). Moreover, each quadrant of each unit is numbered 1 through 4. So, it's generally easy to specify local maps, and to locate things within them.
The defining features are (1) their relative geomorphicness, and (2) the presence of "dead spaces" which represent sealed rooms, fuel space, whatever you need them to be. Since they're 8.5 x 11, I only had to design them to fit top-to-bottom, so they'll work right-side up and upside-down, but if you turn one on its side all bets are off!
I didn't 'customize' each unit, because I wasn't that creative. Also, having the thing resemble a maze of cold passages, all alike, preserves a sense of "where the heck are we?". But I'm thinking there are COTI people who might be able to improve vastly on my idea.
If you're ambitious and doing a huuuge deckplan setup, I recommend you:
1. divide the ship into named regions
2. have each region being no more than 20 units
3. each region only uses each unique board at most once
This lets you uniquely identify and recall any portion of the ship's map, plus lets you, if necessary, note the unique locations of things found. And the players may want to remember something, in which case you'll be glad you made every location unique and recoverable.
I'd also recommend you allow some random method of determining which unit comes next. The deck layout itself doesn't seem to be nearly as important as what you put IN the ship, and where you think it ought to be.
In other words, all you really need to decide beforehand is where the important parts of the ship are --
1. engine room,
2. bridge,
3. armory and barracks,
4. spinal weapon access,
5. bad guys,
6. control panels,
7. guard stations,
8. treasure,
9. the brig,
10. local directory ("you are here" - and reveal the entire local map, sans goodies)
11. officers' quarters,
12. cargo hold,
13. kitchens,
14. medical bays,
15. low berth chambers,
16. hangar bays,
17. smallcraft,
18. areas exposed to vacuum,
19. alien monsters,
20. security bots,
21. areas in Zero-G,
22. etc
-- and locate them by region and, say, a specific (or even random) unit letter. Then as the players explore, you randomly roll for the unit they've just entered, and if it corresponds to a place where some goodies are, then you present it to them.
I'm pressed for time but did a quick look and can't see it. It could be hiding in plain sight though and I'd miss it the fog I'm in at the moment 
