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This is going to be a more straightforward process if you’re using the H9 Control app. There is a System setting to lock in 3 AUX switches, as opposed to an expression pedal, or EXP+1 single AUX Switch.
Last things first, the Looper is standalone, in that you cannot have another algorithm active at the same time. Either-or. Switching between them will clear out the Looper content.
AUX switches are global, in this sense. You can assign them to each of the 10 parameters available in any algorithm [KB0 – KB9]. What that means is a given AUX switch might control Pitch B in a pitch preset, but Delay B in a delay preset. (This assumes you have an H9Max with all of the algorithms.)
You can control the basics in the Looper with 3 Aux switches, in conjunction with the onboard switches. If your focus is largely Looper, it will be more satisfying to go the MIDI route.
After you’ve spent some time with the H9, you’ll settle in to a combination that works the best for you [MIDI with AUX, perhaps adding an expression pedal later].
One semi-advanced option is to tie a single AUX switch to snap between Heel & Toe in your expression pedal mappings. Physical EXP pedal not required. That way, you can program the changes per-preset (like the Performance / HotSwitch options do in different algorithms). Best of both worlds, in a sense.