Poorly, usually. Markdown files everywhere, occasionally a google doc if I'm away from the laptop. Usually hardware projects will end up in a git repo, but mostly for the benefit of whatever firmware I'm writing around it - if there's any specific Kicad integration with version control, I wouldn't know.

The biggest changes I've made recently are leaving notes inside the schematic (so I can't miss them) and keeping local copies of every datasheet and app note that I need.