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My first series of modules was piously positioned according to common logic.
Then, with the newcomers, we worked it out as best we could... we pushed each other, we made room ;)

For me, order is of little importance, since potentially any chain should be possible (except out > out!). This also avoids automatically reproducing the same eternal chaining.

Only common sense counts! Eg. If you're right-handed, a module like Tetrapad will be easier to handle placed to the right of your setup. And vice versa if you're left-handed.

Use long cables (three quarters of my cables are 1 meter long). This makes repositioning easier as you work.
Sequencer > square vco > filter > vca > fx1 > mixer? No...
Lfo > random > sine vco > folder > vca > fx2 > mixer? No, no...
Lfo > random > square vco > filter > folder > vca > fx2 > mixer... Et voilà!