Aim for this: sound up, control down. Try and get your entire audio chain into ONE tier, preferably the top one due to the P/S issue. By putting your modulation, control, etc in the LOWER row, you avoid the P/S noise issue, since induced noise on those modules doesn't really have any consequences to speak of. Also, try and keep your flow left to right up top, and co-locate the modulation sources in the bottom row. For example, if you know you'll be using a certain EG with your VCF quite a bit of the time, then have the EG in close proximity below the filter.
Yeah, it's an effin' puzzle, I know. But it IS the right way to make things work. Go look at an ARP 2600 and you'll see what I mean.