My knees are making me nervous

I've been rotating through Jillian Michaels Ripped in 30 and No More Trouble Zones36 for the past couple of months. I had a trainer watch me do squats, lunges, etc and he said my form was good. I'm getting a little worried about the pain in my knees. Whenever I sit down or squat, the tendons (or is it ligaments?) that run over the tops of my kneecaps hurt a little. I'm not sure what to do...give them a rest for a week or so? Start taking some joint supplements? Wear knee braces of some sort? This sucks! I know I'm getting older, but I'm only 36! This is depressing! Thoughts?