You can really screw up your knees riding with them clipped in in the wrong position (which is why I wouldn't recommend the dual sides, if you already know that the spd's are causing pain).

I switched to speedplay frogs after some knee pain with spds, and have been very happy with them.

YOu could try getting a fitting to see if a fitter can work something out for your knees and fine tune your position/cleat position to help.

If you switch to shorter cranks,it's also a lot easier on your knees. I put 165 mm cranks on my bikes.