Mine used to hurt like crazy probably from squating too heavy and not activating the glutes (no homo). My problem was actually my TFL above the IT band was like a giant knot that needed to be loosened. Laying on a lacrosse ball right above the IT band and stretching did the trick for me. Now the top of my kneecap started to hurt at the bottom of squats. Anybody know if that's usually due to tight quads?
Self-myofascial therapy works fantastic for a lot of people. There are plenty of instructional videos on YouTube demonstrating techniques using lacrosse balls, foam rollers, and stretches for IT band work.
As for the knee pain you described, you may want to consider trying some basic quad stretches. It may also be a matter of squatting too low. Are you lowering past parallel? Some trainers can't do that at all, while others can get away with it for a while before experiencing pain. You may also want to experiment with different foot positions and stance widths.
At the very least, it sounds like a soft-tissue matter. Not that it's a walk in the park, but those types of injuries are usually more easily treated than bone, cartilage, nerve, etc.