I thought about this a little more ... I've been doing it for so many years it's kind of natural and I don't think about it much.

When cleat rotation is off, the feel is as much in my foot inside my shoe, as it is in my knee. I might not notice it until I get knee irritation, but if that happens, it's my foot as much as anything I'll be paying attention to.

Fasten your shoe slightly loosely, get on the bike and clip in, relax everything and let your knee and ankle track the way they want to, and feel which side of your shoe your toes are pressing against. Then rotate the cleat so that your foot naturally wants to center inside your shoe.