More important than anything is arranging them so the stuff you're going to use while playing and performing is readily accessible and not buried under or behind cables. Don't be afraid to turn a module upside-down if it makes it more accessible for you - everything still works the same either way (unless itnhas a . Also, expect to have to make changes to accomodate the ribbon cables and module parts inside the case.
Also, get right-angled cables. They're a big help.