Took me a while to really understand how it all works but hopefully I can explain it clearly enough:
Check out "Stand-In Switches" on pg. 80 of the manual. Basically, they allow you to assign external switches as clones of switches you have configured inside the FM3. Essentially, you would be setting-up switches inside the FM3 as "software versions" of your real-world buttons, and then link them together using the Stand-In Switches menu. Two-button footswitches require a TRS cable and will have both a "TIP" and "RING". "TIP" will correspond to one of the buttons on your external switcher, and can have both a tap and hold function like the standard FM3 buttons, and "RING" will correspond to the other button, and can also have both tap and hold functions.
1. Select two unused switches in any layout (for example, Switch 4 & 5 in Layout 8:Utilities), and program them for the tap and hold functions you want for your external switcher. Let's say:
Layout 8, Switch 4: TAP, (anything you want) HOLD, Preset -1
Layout 8, Switch 5: TAP, (anything you want) HOLD, Preset +1
(I strongly advise against setting preset changes to tap functions, for the obvious performance-ruining reasons.)
2. Using the Stand-In Switches menu, select Layout 8:Utilities, Switch 4 for TIP, and Layout 8:Utilities, Switch 5 for RING.
3. If they're backwards, flip them!
So at this point the FM3 has basically linked your external switches to the functions of those two switches in the Utilities layout. The functions are global and will apply for all presets. You can basically consider this as a sort of default for the way your external footswitch operates. If at any time you wanna change what your footswitch does, all you have to do is go in and modify what the switches you linked to are doing. Make sense?
The cool thing is that you can gain a ton of flexibility and change what the switches do on a preset-by-preset basis by using Per-Preset Switches (pg. 79). Per-preset Switches essentially swap out any switch in any layout with any other switch functions you need. Example:
1. Let's say that on a particular preset, you'd like your external switches to have some different tap functions than normal, and you want your external switches to perform Scene -1/+1 on a tap, but still do your normal Preset -1/+1 when held down.
2. Go to the Per-Preset FC menu and program two of the slots as new switches with the functions you want. You'd organize them as two separate buttons, similar to how you did before, but this time on the Per Preset FC page:
PP#1: TAP, Scene -1 HOLD, Preset -1 PP#2: TAP, Scene +1 HOLD, Preset -1
3. Then, by using the Per-Preset Overrides menu (bottom right of the FC Controllers page on FM3-Edit), you instruct the FM3 to "override" the switches that your external buttons were linked to. You would select Layout 8, Switch 4 and override it with PP#1, and override Switch 5 with PP#2. And just like that, the functions of your external buttons will be different for that preset only. Switching back to a different preset will restore the normal functions of your external footswich, or change to whatever you need for that one, too.
Okay, hope that makes sense!