First you need to go to Setup, IO, Pedal. Then you setup the switches based on their polarity. It sounds like you already have this as you have them controlling FX.
Next go to settings, FC/Onboard switches, and page along to stand in switches. Here you basically point the switches to an existing layout - they then trigger that layout function whether the FM3 is in that layout or not. I chose the Perform layout because it’s a layout I will never use and so am happy to edit the functions in there without breaking other layouts. So I selected Layout7 and switches 1,2,3,4.
Next, still in FC/Onboard, scroll to layouts, scroll to layout 7 (if you chose that) and hit enter to go into that layouts settings. Set tap on 1,2,3,4 to the function you want - mine controls scene 1-4, then page over to hold and set that to what you want the hold functions to be, mine set the onboard switches preset switching or per preset switching depending on what I hold, or inc/dec a preset.
Photos of how I set each screen attached.