The Knee pads that I use has a gap on the back of the Knee. This is good because in suwari waza & seiza we sit down fully with our foot and toes flat on the mat. This type of knee pads actually give good room for the fold of the back knee. I've tried other knee pads eg Judo knee pads and they do not leave enough slack on the back for a folded knee, the crease can rub and sting after a long use specially if get's hot and sweaty.
I also found that mats can make a big difference. Mats that have a dove tail joint on its sides and have a same rubber texture as thongs/flip flops has a very good grip on it. I've noticed that I hop with my knees on these ones rather than slide and glide through them. They are really hard to do suwari waza, shiko, and hamni handachi on. There are a few times that I can really feel my knee caps twisting on these hard core mats. Mats that are made of shredded foam with a tarpauline cover on is friendlier to the knees due to less friction. This is the same with Vynil covered mats. I've noticed that Tatami mats are in between the rubber mats and the tarp/vynil mats on the account of friction and resistance.
Having said that I wonder how are the knees of aiki and ju practioners that do suwari waza on grass, sand, wooden floor, or... concrete.