What kind of pedals did you get? They should not be that hard to get into!

I sometimes have a little trouble clipping in with my second foot with my Eggbeater Candies, but I think that's mostly because of the uneven-ness of the trail. It's hard to coast long enough to get clipped in. I never seem to get my foot in the right place, or it takes longer than it does on my road bike. I clip in just fine with the first foot.

A friend recommended Speedplay Frogs, saying they are SUPER easy to clip into. If it's not too late, maybe you can exchange your pedals and try Frogs instead? They also offer a ton of float, which might help with the knee pain you're having.

Good luck!

Emily