Adjusting feet braces in prism

I keep hitting my hands on my knees with kayak paddle in my prism. I guess my foot brace is too close? Should your knees be below the gunwales?

Well, if you are hitting your knees, either lowering them or keeping them further inboard should help. Most solo paddlers who paddle seated seem to have their knees higher than the sheer line, but you can certainly have them lower. Another option is to add a pair of minicell knee bumpers like these:

Minicell is easily shaped using surface forming tools or sandpaper. If you wanted, you could shape out a concavity that fit your knees and gave them some fore and aft support.