During squat your toes should point outward and knees travel over your toes. You do not want them traveling inward, ie collapsing. In regards to the popping, maybe do moe warm up sets to get the fluids in there and joints warmer.
In regards to the subluxed patella, you need to speak with a specialist about that. If your patella is back in place, you should be OK, however, if it didn't go back correctly, you could really damage your knee. Unfortunately, once your dislocated a joint, you could be more susceptible to it in the future if the tendons and ligaments don't tighten up.