I ride on KEO's with Sidi Genius 5's and love the combo. FWIW, I have my cleats pushed virtually all the way rearward on my Sidis. I am also slightly slew footed and you want to adjust the cleats kind of like you walk.
For me, like all bicycle fitting, it takes extensive trial and error. And...each foot is slightly different. If I put the cleats in the middle of the travel of the shoes, I can't get the energy to the crank. Pain in your knees can be a multiple of things...saddle height, set-back...even the cant to your cleats...you may need shims either inboard or outboard if your feet are naturally pronated or supinated. If you can't figure this stuff out by reading and/or experimenting, try to find a local cycling coach and pay to have your pedal stroke evaluated.
Good Luck,
George