Welcome to the wonderful world of cycling, I hope your knee pain doesn't slow you down too much. Can I ask how you know its IT band syndrome you have? (I ask because I am an Orthopaedic surgeon) There are lots of causes of knee pain, you see and it depends if its the IT band or not. If you do have it and you are most comfy with the knees close to the top tube it may be that you have some hip anteversion as the underlying cause. Don't worry that's not a disease! Its when your neck of femur (the bit attaching the ball of the ball and socket joint, to the rest of your thigh bone sits pointing more forewards than some.) Sometimes it results in in-toeing, but sometimes the shin bone adapts and grows with a twist to keep the toes pointing forewards. Either way this is all part of the rich variety of body shapes and biomechanics that we blessed with and what makes us all different! If either is the case you will be more comfortable with your knees inwards and to fight it may also add hip pain to your troubles!
If you are an "in-toeing" individual you just have to make sure that any cleats you have put onto your shoes for clippless are pointing right for you - forcing the foot out will definitely make your knees hurt.
Clipless are brilliant and you will love it once you are used to it. You will go faster and fatigue less..... You might consider pedals that allow some "float" which means there is some give in the amount of twist your foot can do and its not rigidly fixed.
I hope this helps. Good luck.