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Having just spent a few days trying to figure out the configuration possibilities of an aux pedal, I'll try to help a bit.
I'll try not to misinform you but caveat emptor.
1. The aux assignments are specific to a FUNCTION not a PRESET. If you have the tip assigned to BYPASS it will perform that function on any preset. But first you have must select that preset.
2. The FS1, FS2, FS3 functions are a bit confusing. These assignments allow the aux pedal to perform the functions of the unit's switches of the OPPOSITE mode of whatever you've selected on the unit. Meaning: if you are in PLAY mode FS1 will perform the function of the left footswitch as if you were in PRESET mode. Another way to look at it: If you have FS1 FS2 FS3 assigned to your aux pedal AND you are in PRESET mode, the aux pedals will respond as though you were stepping on the switches on the unit while in PLAY mode. If you are Bank mode any switch assigned to "FS1/2/3" will respond as though you are stepping on the switch in PLAY mode.
3.Any switch can be assign to any function through the system menu. Multiple assignments can be made to each switch and are sometimes necessary .
Here's what I just spent 3 days learning (I have TF, PF and Space): For Space I wanted to be able to have ONE aux switch select the next preset AND activate it. Presets (as you probably know by now) don't activate just by being selected with the aux pedal. Here's where it get's interesting:
I have PRESET+ assigned to Ring (it doesn't matter whether it's tip/ring/etc, that was just my choice). I have FS1 ALSO assigned to Ring. I put SPACE into PLAY mode (very important).
When I now step on the Ring footswitch it steps the preset up 1 selection AND BECAUSE I AM IN PLAY MODE it also activates that preset (because I am also "virtually" stepping on the ACTIVATE pedal of PRESET/BANK mode simultaneously). One click to select and activate.
Brain spinning? Mine too. The power to control these pedals is very deep. As I said it took days to figure this out and I have 30 years of this stuff under my belt. Or I'm just stupid!
I hope this helps. Sorry if it's not clear enough but I type very slowly.
Don't give up!