If you're just asking about cutting a hole in the pulpit, which it sounds like you are... pretty basic and straight forward. Cut the hole, reinforce if needed inside the cavity (I'm assuming the pupit is cored otherwise you probably wouldnt be asking about this), seal it up with epoxy, go fishing. There's little things like using a drill bit at each corner of the hole to prevent spider cracking of the gelcoat, but if you're up to the task of doing this yourself, you probably already have decent woodworking skills so those kind of things you would already know.
But... will you still have room to mount the trolling motor? I would think that there is very little real estate left forward of the hole. I also imagine it won't lay completely flat because of the windlass, so account for that with a strap/modified rest.
Have you thought about just building a simple angle adapter plate to mount the trolling motor slightly off center?