Well, my process is generally just coming up with an idea, drawing it out, and then executing it.
To use this as an example, here's the diagram for Tidal Palace, probably the most themed map we have, on paper:
http://mystic.sepwich.com/image/scans/Scan_Pic0002.jpg
This was drawn out before the SRM/WRM system was implemented, so here are what the abbreviations mean:
1F/2F/B1 - floors
SR - Super Ring
*W - Weapon panels. (AW = automatic, etc.)
RM - Random monitor (At this point in development, we were actually using the ? box as our only random monitor type)
What you'll notice by looking at the basic design layout, though, is that the stage gimmick really doesn't have much to do with the layout. The layout was designed with water in mind, but it isn't like the entire stage is built around the gimmick. It's just a normal stage the floods every once and a while.
You'll notice a huge amount changed in development as opposed to design. The water flow gimmick in the original is shown with the drains and waterfalls (originally the idea is that the players in the game could actually control the water flow by destroying things blocking the input and output). There was an additional (boring) passage on the west end of the map, that was replaced with the passage in the water next to the automatic tile because the stage felt too large. A lot of minor details in the rooms were changed because it felt too uninteresting and uninspired. Also, almost ALL the weapon locations were moved, and so was what became the SRM.
The REAL key to making sure your level plays well is tons and tons of repetitive testing. I'm pretty sure we played this stage upwards of 100 times back in testing to make sure it played well, tweaking the item locations and sector layout to fit with the problems found in the playtesting. It's a lot of work but it does result in a better end product.