I like to set up my "thigh/Knee" braces so that they actually support my upper leg ( thigh ) Just above the knee, i find it some what un comfotable to have pressure on the knee itself.

I have just glued minicell foam into my inside my cockpit under the deck. I have also made "keyhole" cockpits. which is best depends on your size relative to the cockpit size.

if you can sit in the boat now, check out where your legs end up when they are in a location that you find comfortable then decide if you can just glue in a bit of foam or need to build some plywood structure (keyhole fashion) to brace against.