I have dodgy knees, try not to skip on hard/solid floors, skip in the ring. If you can do your running on a treadmill or running track do that. Lots of trainers will think you're trying to get out of the hard work. If they hurt doing squats then check your technique, don't jerk or snap your knees back, very bad, also don't bend as deep.

For some reason my knees just kill if I do lunges, it's one of those things, I just can't do them without knee pain.

You might want to start taking glucosamine supplements & iceing your knees after every workout. Glucosamine has been shown to help repair cartlidge. Ice will take down any swelling and the increase in blood afterwards with flush the joint.