I believe that with any meditation, one of the keys is relaxation. I would say break from tradition and get comfy. There are many different forms of meditation. If a zen moment is what your looking for, pain will help you in the here and now. If you are looking to get really internal, than I wouldn't want to be distracted by an external element. Ki development or anything with ki, concentration is paramount. If you are breaking concentration, than you are not getting deep enough.
I think that the discipline developed by just making time to meditate is enough. I don't feel that I need to make it more complicated than it all ready is. Havinmg achy knee's or just being generally uncomfortable might be enough to stop meditation all together for me.
-Chad
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