Do about 1 hour of shiko around the mat. Then sit in seiza for 20 mins, then repeat. (or alternatively use a concrete floor).
If this doesn't damage your knees nothing will.
...seriously; I find just doing shiko and seiza regularly will help you stretch. Also sit in seize and then lean back until you feel the stretch (try to get your head to touch the ground behind you). Try to warm up your knees before doing any of this (light stretching) as you'll end up with knees like mine (I can use the cracking of my knees instead of a verbal kiai to get really good kokyu nage).