Before hard wiring your rig hook up the pedals to your switcher in the order you want them and manually (by pushing the switcher's buttons) check them individually and in the sequence that you want to run them. Live with them for a day or two before committing. While there are some basic tenets of how they ‘should’ be ordered (check You Tube for suggestions) it’s really a matter of taste and what works for you in your particular situation. When you’ve settled on what you want then ‘rack ‘em up’ and start programming your presets.

With matrix switchers like the Mastermind PBC/6X, it's even easier - you can change loop order in the switcher's settings, and even change loop order from preset to preset.