Hello Girls!!

I bought a bike about a month ago from my local bike shop. I had it custom fit since I have an existing knee problem (IT band syndrome). I have being very careful not to hurt my knee. I have so far done close to 100 miles (only run one time a week, 20 miles each time since I don't want the monster to wake up -the pain). I use very low gears for climbing to keep the beast asleep (knee pain) and also because I am out of shape . I wish I could go faster but when I increase gears my knee starts acting up. I have a few questions 1) Should I consider "clipless" pedals? Is it true it might help my knee? Which ones should you recommend? Shoes? 2) Am I doomed for having IT band syndrome? 3) Those with preexisting knee injuries or problems? How you do it?
I am tired of putting off exercising because of my knee and I want this to work for me. I am so ready to get more active and lose weight!! I have a Specialized Sirrus road/commute bicycle and I love it. I am still getting used to the shifting gears, etc. One thing I noticed is that when I pedal having my legs almost touching the upper pole (like in the Tour de France) I do not feel any pain when accelerating or using a higher gear!! You don't know how happy I was, I was flying today! Of course, I am concerned since I do not know if this is the proper way to pedal. The weather was windy and cold which made my knee hurt a little but I know to use longer cycling shorts next time. As soon as I am done using the bike the pain stops (and the heartache starts, I LOVE MY BIKE!!! ) Please, somebody help!!