Knee Issues

This year has been a struggle for me and my weight loss, I feel like I put so much effort in and get little results. I started the year with a hernia surgery, and about a month after my recovery time was over and I was back to running, I broke my big toe. Which doesn't sound like too big a deal, but it's very painful to run on!
I have been doing more cycling classes and more weightlifting, still unable to lose more then 5 lbs :(
Then the first week of July while I was running I noticed quite a bit more shin pain then I've had in a while- other then that I don't recall any trauma to my legs or knees. But by Friday the 9th as some friends and I were driving to Shreveport my knee was killing me! Not only was it painful and swollen, but hot to the touch. I took a picture, and it looks like I have two knees! I went to the doctor on Monday when I got back, and he said it was Prepatellar Bursitis, "water on the knee".
He didn't know how to drain it, and the orthopedic surgeon couldn't get me in for another week. He did give me an antibiotic, which did nothing for the pain, the heat, or the swelling. By Wednesday I went to the ER, thankfully because of my surgery earlier this year my deductible is covered and everything is free for me. The ER wouldn't drain it because after an ultra sound they were afraid that it was infected. He gave me really good pain medicine, told me to keep ice on it, and stay off it as much as possible.
RIGHT!
I have 3 kids at home this month, and I'm working! The only way I made it though my work shift was to have two ice packs, one on it all the time and the other one refreezing after use.

By the time the Orthopedic Surgeon saw it, he suggested that it might not be infected, but he just wanted to keep an eye on it. A week later he said looks like the swelling is going down, just don't kneel down for a while.
The swelling is mostly gone now, as is most of the pain. I still can't kneel on it, and the fluid sac that you could feel is mostly gone, but it has been replaced by hard bone. My fear is that my disease has kicked in and once again grown more bone in a very unsightly area. I might just have two knees now :(
I think I will keep my exercises away from running, as to avoid any knee replacement surgeries in the future. I looked into adult swim teams, and gawked at the price.
Cycling classes it is!