I encourage you to review the
Squat Rx videos to help learn good squat technique. I think you'll find that you're knees will improve as you increase your hip mobility and leg/hip strength.
And I'll say again what everyone else has mentioned. If you want to be bigger, you have to eat sufficiently to gain weight. You can't have bigger legs without gaining weight and without giving your body the nutrients to use to grow muscle. No amount or type of exercise will make you grow without excess calories.