Squats after bursitis diagnosis-knee pops

I am 26 years old and was recently diagnosed with bursitis after a direct fall on my knee. They did this using x rays to determine there was fluid behind my knee. It has been a long road of recovery in the midst of trying to do the p90x program with the insanity program. My husband and I took an entire week off to see if I could exercise without too much pain and I think it helped. I am still having pain when doing high impact jumping and doing jump lunges so those things are dialed back, but the problem I still seem to be having (present since diagnosis) is a clicking in my knee when I do squats. The pain increases gradually if I keep going but it isn't anything emergency-like. Has anyone else experienced this and had it eventually go away? Are there any exercises to therapeutically strengthen the knee to reduce the fluid under the knee and/or strengthen it? I would appreciate any comments.