Hey, Jayme. About a year and 3 months ago, I ruptured the patellar tendons, which hold the kneecaps in place, in both legs. I had emergency surgery and was in the hospital for 3 weeks, in braces another six weeks, on a walker and crutches for several months, in excruciating pain for many months, etc.
And the surgery was botched. Both my kneecaps moved up, so that when I sit, they face upward rather than forward. It's called "patella alta." "High kneecap." Eventually, this will likely create unbearable arthritis and I will have to have the surgery done again. In the meantime, I cannot walk downstairs without considerable pain and difficulty, and ordinary squatting, even sitting down, is often painful. Otherwise my movement is unrestricted.
I was back in the gym two weeks after I got out of the hospital. The injury hasn't affected my upper body workouts. (I also did a couple months of rehab. I had miserable rehab therapists who did more harm than good through their ignorance and laziness. I won't go into all of that.)
I found that I can compensate for not squatting in a variety of ways. I use the abductor/adductor machines and others that don't stress the knees. I've completely maxed out on them, so I have to do ridiculously high volume. Also, leg curls do not stress my knees, since they are supported during the movement. As is usual in such injuries, my hamstrings have grown to compensate for my weakened quads.
For directly working he quads, I do leg presses, often one leg at a time (this seems to work better; why, I don't know). As I've said in a zillion threads here, I use HST. It works on the principle that the actual weight doesn't matter as much as the progressive addition of weight. So you calculate the maximum weight you can bear and then back it up x number of weeks, so that you progress slowly to it. It is gentler and more effective than other training methods:
Although it is not designed so much to increase strength as size, I found that it fits my compromised strength training very well.
Finally, I should mention that after firing my loser rehab therapists, I hired a private yoga-strength trainer. She was especially helpful in recouping strength in my stabilizing muscles.