In my own canoe, I sit most of the time and only drop to my knees when it is very windy or if I am in rapids. I'm also lucky to never have had a serious knee/foot injury, so none of the discussion about knee or ankle pain while canoeing has ever really resonated with me, thankfully.
This past week, however, I borrowed a friend's canoe with a saddle seat and thigh straps. This was my first experience with that kind of set up. Three and a half hours of constant kneeling later, my knees were ok (even though his saddle was a bit low for me). But, oh, yeah, my ankles were definitely sore and my feet were tingling and well on their way to being asleep at the take out. If I ever paddle a boat with a saddle again, I'll try the pool noodle or some foam pipe insulation under my insteps.