i have been having knee pains with both knees for a couple of months. The pain is located below my kneecaps. I went to the doctor to see what was wrong the first time he said that it was my meniscus and that a few days would cure e which ended up happening. Recently I played basketball and my knees started to hurt again 2 months laters i tried the same rest method but it didnt work this time.
I tried squatting and i ould do it without with pain. i even have trouble squatting without weights. I wanted to know what I could do to substitute the exercises and still have my legs get a decent workout without receiving too much knee pain

Well your first priority should be to get those knees back to full health.

Something is obviously causing the issue, and with the knee there are usually numerous problems that could be causing it.

With the reading I have done, the first things to look at would be ankle mobility/flexibility and whether or not you have an underdevelpoed VMO (vastus medialis):

http://upload.wikimedia.org/wikipedia/commons/3/38/Vastus_medialis.png


Here is an article where Poliquin talks about a weak VMO and prehab/rehab exercises you can do for it.

http://www.biggerfasterstronger.com/uploads2/PreventACLInjuries.pdf


Look up t-nation articles by Mike Roberston and Eric Cressey, they have some good articles on these kinds of issues.

You could also consider buying Mike Roberstons ebook, I have heard good things about it:

http://www.bulletproofknees.com/

For the pain/swelling put some ice in a plastic bag and put it on the sore area. Don't do any exercises that aggravate the pain and then after a few weeks see if you can slowly work the exercise back in.

Just out of curiosity, are you the guy I got doing box squats earlier in the year?

Sit back instead of down. And go below parallel.