Hi Kate,
I also have bad knees some days. I have a re-occuring injury from a car accident, that makes my knees very uncooperative at times. Depending on what parts of your knee hurts, depends on if any of this will help.
If you are kneeling with the tops of your feet flat on the floor, I have found a rolled up towel behind my knees/on the back of my calves helpful. Also good for the posture.
I also find not sitting all the way back on my feet to also help but this involves a lot of core engagement and depending on strength can limit the time you can hold this position.
Another thing is spreading your knees while kneeling. I have a very hard time if I am kneeling with my legs/knees together so my Dom makes me kneel with my knees/legs wide and my hands on my thighs, palms up. I find this position very comfortable and can hold it for quite sometime. It is also quite nice to lean forward with my arms stretched above my head in a Childs pose or something similar to show my submission while also being comfortable.
One last thing I have found to help, is a folded towel under my knees. So kneeling down onto a towel/cushion rather than the hard floor.
Part of the issue for me is the way in which I choose to kneel down. After many attempts and many hours of practise I have found a way that is slow enough for my knees but still allows me to feel sexy rather than awkward. If I drop to my knees that is very painful but if I bend one knee as I stretch the other leg out behind me, I can slowly lower myself down and then once balanced on the stretched bent leg, I can then lower the other leg to complete the kneel before opening my thighs and lowering my hands. I hope this makes sense! After much practise I can now to it with my hands on the back of my neck.
But enough rambling from me and I hope this helps or at least gives you and your Dom some ideas!
Much luck,
-Maddie