The best thing I found was to try and sit in seiza more often. This helps to get used to the position and will also help you to find your "sweet spot". For me that is with my weight on top of my feet with the ankles pushing out.
Outside of just sitting in seiza try to stretch out quads before and after as that also helps with position. - Disclaimer my issues with seiza was tight quads.
Further investigation has yielded this video on how to practice seiza. It covers the use of pillow to help support your weight (between the legs, not underneath) and various stretches.
I also uncovered this forum post which again offers a variety of methods for practising seiza. Unfortunately both involve sitting in seiza which could constitute to "Do more of it" and neither are peer reviewed or sourced. Hope it helps though.