Right- if you want to bottom-mount the stick, but it's too low on the top side, you'll need to use a router and route out some of the wood so it's higher.
Depending on the thickness of the wood will affect how much material you can eliminate. There are numerous threads in the Woodworking forum that talk about bottom mounting (or under mounting) joysticks.
Another option, for certain sticks, is to get longer shafts.
Ultimarc 360s and Sanwa JLW sticks can both use the long shafts that Divemaster sells.