My best advice for suwari waza is: don't do it. It's just bad for your knees and body. It's one of those things we do because we're told to do it (aka "tradition"), but other than "tempering the spirit through physical punishment" there is little to no martial benefit from training suwari waza that cannot be achieved standing. Mind you, I did a lot of suwariwaza in aikido... I'm just doing less and less of it these days as I try to avoid destroying my body like so many aikido veterans have.
Personally, I don't think that it's really a tradition - it's a combination of smooth canvas mats (which encouraged the practice) and young students (whose knees could hold up to the training) after the war.
The young guys on smooth mats introduced a lot more movement than existed previously. If you look at Daito-ryu and other traditional schools there was very little of the moving around on your knees that you see in Aikido today.
Yasuo Kobayashi used to say that he was the one who introduced shikko as an exercise - in the 1950's.
People today are paying the price with their knees.