It depends on which pots but I'll assume something like an Alpha RV16AF.
3PDT toggle switch body height's are usually a bit taller than the pot leg length. If you include the lower nut and lock washer, the difference is a couple of millimetres. Either way, you need to extend the pots somehow. The easiest way is to extend the lugs as Jim described (but on the pots not the switch). You might also be able to get them height aligned if you mount the switch without the lower nut, and add a washer to the pot (I use an M7 lock washer). That should get you close enough so that the pot lugs are through the board and can be soldered properly but maybe not quite all the way in. Just make sure you have clearance between the pot body and any solder joints below it on the PCB.
Mount all the hardware to the enclosure (or build a template from 1/8" hardboard or similar) and then solder. If the switch is shorter (which is the case with SPDT and DPDT toggles) solder the switch first before mounting. This is so that everything is sitting where it should be and the positions don't shift (and stress the joints) when you do the final assembly.
When it's the other way around (SPDT and DPDT toggles shorter than pot) I use the toggle's bottom nut to bring the overall height to the same as the pot plus a lock washer. I solder the switch first, then mount the pots in a template and attach board and solder. For final assembly, after tightening pots, I adjust the lower nut of the switch until it is just snug, and then tighten the top nut.
I prefer to use pots with lugs rather than the right-angle PCB mount ones. I use solid core wire for leads, and this lets me adjust the height as desired.
