Everytime I squat I could hear my knee cracking. The raison: my miniscus is damaged. But I still squat, more than ever! I'm doing powerlifting comp, so I put alot of weight. Make sure that your knees doesn't go inside > < when you're squating. (too much pressure on the knees) Also, make sure that you keep your head up, never look at the floor.
Do alot of leg extention to bring your quad stronger. Don't forget to do some warm up (like light leg extention)
LG