I have problems with petelar tendonitis also, i play ultimate as well as ride, and it gets bad sometimes when i do alot of both. A couple other things i've found helpful.
since you just switched to riding fixed, Check your setup and positioning on teh bike, especially saddle height and position. Saddel too far back causes me problems, i use a 0 setback seatpost and that helps. Also, I am an over pronator, and have a great deal of varus(when running or pedaling, the outside strikes first, then the foot roles inward=bad for knees) Lemond makes this product calle Lewedge that helps. It is a set of shims, that fit between the cleat and shoe, so that you push at the proper angle, felt alot better after using them.

And when it hurts. You have to rest it. It will only hurt more.