Quads hurt = good, you're working your muscles differently and will get even stronger

Knee hurts = not good. Do your cleats/pedals allow float (i.e., can you move your ankle right and left a bit without clipping out)? I am not sure what type of cleats you have, but some allow a lot more float than others. In mountain pedals/cleats, Speedplay Frogs allow the most float (28 degrees). I use Eggbeaters, which say they allow only 6 degrees, but it feels like plenty to me, and no knee problems.

It is also possible that your cleats need to be moved slightly to make your knees happy. I have heard that you should sit on a hard surface where you can hang your legs down over the side and see how your feet naturally fall (straight, pigeon-toed, toe out?), and try to seat your cleats a bit that way. It may take some experimentation.

Good luck!!! Glad you're doing better with them, aside from that. I started right out mountain biking with Eggbeaters because I use clipless on my road bike and can't imagine riding without them, but I know being clipped in has given me problems at times on the trails. I am determined to ride with them, though, even if it takes me longer to conquer Crabtree than without them! They definitely help me on the climbs, but I have to bail out of them a lot since I expect to fall more often than I do.

Emily