I go back and forth on this as well! Up till now I have been looking at the two cases as a single unit, which tends to observe top-down arrangements: Oscillators and sound generating devices in top rows, then, row 2 processing modules, row 3 would be clocks, VCAs and in general modules that control/define structures, and finally at the bottom the modules that function as interface, or require special manual control attention.
This is just a general frame of reference I use, but in reality there are plenty of exceptions.
Having said that, I have been thinking a lot about having the two cases also function as independent units, so am contemplating a re-grouping project eventually.