thanks for your input everyone
i'm 16, the pain is usually in the front more towards the inside of my knees after i ride. They really hurt after sitting for long periods of time, i find it hard to stand up. After i get moving it generally goes away. Its usually just feels like its really sore. i don't usually stretch. I think thats it
I'm gonna throw growing pains up there since you are only 5'3" and 16, but the cowboy stance mentioned above may have some effect. I would focus on how you are bending your knees. Think of a straight line going out from your heel to your toes on each foot. When you bend your knees, try to keep them following that line. I would widen your stance a bit, because 18 inches is pretty short. You wanna go at least a little bit wider than shoulder width. Just make sure when you bend your knees that they are not getting any closer together. Check out "medial collateral ligament or MCL" on google and see if any of that makes sense. This is a page on injuries but it is just a start --> http://www.nlm.nih.gov/medlineplus/ency/article/001076.htm
I would guess that when you bend your knees, you are bringing your knees closer together, putting excess pressure on the outside of your knee, and stretching the MCL. I know this pic is weird, but if you imagine a line drawn from the hip to the knee, and another line from the heel to the toe, they are both pointing in the same direction, so no extra pressure or tension is put on any ligaments of the knee.
You don't want your stance nearly as wide as the guy in the pic, but the knees and toes pointing in the same direction is important. What I think you are doing is squeezing you knees together in a way (closer to the blue weight in the pic) which causes undo strain on the MCL.
Stretching is a big one and can really help. Quad, hamstring and calf stretches for sure. Also doing some hamstring exercises helps. You pretty much use your quads all day and your hamstrings very little, so if your quads start overpowering your hamstrings too much, you can get some pain (although I believe what you are experiencing is not caused by this, and is more of an MCL thing.)