Anxious to hear everyone's answers on this one too!

Have you guys tried using those small routers with a foam router bit?

I place the gel pad on top mark out where I want it. Cut out the entire marked out section.
Try and cut out an inch from the middle of the piece. Glue up the sandwich back in the rest of the foam. I also usually add some scrim foam to the top before putting the cover on.

So I came up with a good way to do it. Take one of those cheap knives that you get at the hardware store. I am talking about the ones with the break off blades. Measure the thickness of the gel pad. Mark that figure on the blade with tape. Cut the perimeter first then make a ton of cuts in two directions.. Never let the blade plunge deeper than the tape line. You will end up with all these little boxes that you simply pull off sideways and Wahla you have a nice uniform bed to lay the pad in.

Check out this how-to article we published in 2012: How to Install Motorcycle Seat Gel Pads