LEFT = UP, RIGHT = DOWN. Control signals start on the bottom with sequencing, MIDI interfacing, soundcard I/O, etc, then go up on the left along with modules to work with them in that path. Generators (oscillators and their pals) on top, as they're less likely to be tweaked while playing. And filters + FX go above the final output mixer, sent down the right side from the top. Modulators, if left in the middle, can then branch out to anywhere in that circular flow with a minimum of cable-snarl. And putting the FX right near the final mixer makes them easier to add to the mix. So, even though there might be several "instruments" patched up on a single synth, you're able to follow what's going on with the patches more easily.
-- Lugia
Yup! That's exactly the layout that I've found has worked for me (and probably will work for others).