No rule, I simply try to fill each deck with appropriate stuff and leave enough room to walk around. Like the KH book describes I can still hand-wave the "between decks" areas as room to stash whatever doesn't fit in the deck, such as the rest of a generator or gunnery station etc that extends up/down through the ceiling/floor.

I start having problems with big ships though, simply put there's far too much available space and not enough "stuff" to occupy it. My biggest deck plan to date is a HS:7 vessel (the Timeon Clipper), I started a UPF Light Cruiser once and had an overly elaborate bridge that only filled half of the smaller top deck and gave up on it realizing I would not be able to render 20 decks and accomodate the "small" crew associated with such a massive amount of space. An equivelent sized freighter might be doable since a lot of it is cargo hold, but still...it's an awful lot of space to utilize for an even smaller crew.

Also, for those that may have missed it, my Mark II Assault Scout is conveniently perched above the two capital ships in that section.