From the discussions I've seen, a good rule of thumb is to measure from one row of windows to the next decide that you need 3 or 4 meters from the bottom of one deck to the bottom of the next, then work everything backwards from there.
But that doesn't always work out either, for example, some references have the Reboot Enterprise at is roughly 1200 feet long, but that would make the shuttle bay too small for what was seen in the film. However, using that shuttle bay to determine scale makes the ship about half a mile long.
Sometimes I have to remind myself that despite the best efforts of the designers/FX people, the ship, or anything else, looks the way it does because that's what the person writing the check wanted it to look like. Or in the pre-CGI, that's what they could build that would bear its own weight on the budget they had.