I'm another whitewater-head, so even my flatwater boat has a saddle and knee cups - I just find that more comfortable, probably because it's what I'm used to. Before I went that far, I used to toss an old piece of an ensolite sleeping pad in there. That was comfortable enough, but it slid around once things got wet between it and the hull, and there was no way to avoid stepping on it when getting in and out.
Knee pads always seem to bind and chafe behind the knee - the ones OU keeps on hand for canoe class students to use seem to only get used the first day.
I suppose you could try a pair of those neoprene knee support sleeves that drug stores sell, though most of those have a hole where the kneecap goes. Maybe cut the back out of it, to eliminate the chafe point, then glue the resulting piece onto the front to close up the kneecap hole? :)
Canoe / Kayak Anchors
Touring Kayak Paddles
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