I have the same issue. Sore knee's and a fair amount of clicking.
I also saw somebody about this, and what kyle has said, is basiclly word for word what i was told.
I was told to ice everynight, and do excercises to help strengthen the inside of my thigh to help the knee cap track properly.
The excercise i was given is as follows:
*Sit on floor, with legs straight out in front.
*place a rolled up towel under your knee, so the underside of your thigh is about 100mm off the ground.
*Pull the knee cap up, then raise the heel off the floor so your leg is straight.
* lower heel to floor, relese knee cap
She told me to do 5x10 on each leg and ice after.
It doesnt feel like it does much, but my clicking has imporved. Strap a bag of rice or similar after a few weeks.
I also found that getting the knots/tightness brutally massaged out of the outside quad help ALOT also.
She told me not to squat anywhere near 1RM, and told me to 1/4 squat.
So i worked on my 20RM which went from 80kg, now to 102.5kg @ 80kg
Hope this helps, sorry for the uber post!
P.s I take 15 fish oil tabs a day, do they help, maybe. Wouldnt really like to find out.