Try to spend some time each day just sitting in seiza. back straight, good posture. As a "westerner" who didn't grow up using seiza as a regular seated posture, it will never be as comfortable for you (me too) as someone who, growing up in Japan, has lived it in his/her culture. I understand that modern Japan sees seiza less frequently used - I wonder if that's causing "westernization" of their knees?...
My experience with Japanese - even the older generation, is that seiza isn't really any more comfortable for them than it is for anybody else. They're just a little more accustomed to the idea, that's all.
For example, making school children sit in seiza used to be a popular form of corporeal punishment.