Painful knee and hips with martial arts training.

This problem has been on & off for about 2 years and am now wondering whether I could've caused permanent damage.
I’ve always had clicking hips/ knees since I can remember with not really any pain, just fear something would snap when I bent my knee. I have bowed legs (no idea if this is related to pains) and have learnt my left side is weaker technically since taking up martial arts again 3 years ago(after 13 yr break). Since then I would sometimes over extend either knee when kicking causing pain behind the knee/upper calf. If I took it easy for a few weeks and wore a knee support it would eventually feel better, until I over extended again.

Going for my 1st brown belt meant I upped my training at home and added aerobic DVDs to build my stamina and continued with my stepper (+resistant bands) to build strength. I alternated each through the week; 2x evening karate, 4x evenings DVD or stepper. Each would be between 1 half to 2 hrs.

A few weeks after using the aerobic DVDs I noticed the dull pain behind and to the side of my right knee, especially when bent. It alternated with the other knee, and became a constant pain for another week or so. It then got worse & unbearable at night, with a burning feeling all around the knee cap & inner side of the knee along with the constant pain behind it & the upper calf. The doctor said I’d strained it or something; to take a month off the aerobics and use a knee support. The month off helped for a little while but when I tried to get back into training more at home again, the pain would come back, whether at rest or training and especially when bent sitting at a desk. It would only feel better when there was no pressure on it, with a cushion elevating it and keeping the knee slightly bent.

I'm worried that I’m not stretching or moving correctly, as both hips hurt/click/pop and my right knee (mainly the front & inner side of the knee cap now) hurts when I try stretching or high kicking manoeuvres in karate, even after I have warmed up considerably. My right hip with right knee becomes sore if I walk more than a 2 miles. I’m now really concerned as I have my 2nd brown belt grading coming up and I cant seem to train properly without having to take more time out to let my knee/ hip recover.

Strangely, I hate running but ran 2 miles for sport relief on Sunday just gone, and my knee didn’t hurt whilst running, only when I walked the other 4 miles?? My right hip was excruciating a few hours & a day later, but only if I allowed my self to limp, if I walked properly it didn’t hurt so much? Today hips seem ok, little sore and right knee is just uncomfortable.

I apologise for not being very informed on what it maybe and if I’ve not given enough information or described it well enough, but could someone give an opinion on what I am doing wrong and how to prevent my knee & hips from being so painful so I can train for my next belt? I’ve also thought about supplements/vitamins/minerals for joints, is this actually worthwhile? Your help and advice is greatly appreciated.