I use both brakes until almost stopped, then switch to front brake for the final stop and put down both feet together. You know you are doing it right when you put your feet down and they plant immediately. If you are doing multiple touches before you stop... you are putting feet down too soon.
The key here is being able to balance the bike at a mere crawl with both feet on the boards. I see soooo many riders either stopping or pulling out with their legs dangling. As long as that bike has ANY forward momentum, regardless of how slow, both feet should stay on the board/pegs.
The best practice you can do is get in a parking lot and practice how slow you can go without stopping and with feet completely on boards. When I take my foot off of the rear brake and put down my feet down, I am barely moving so chances front brake only causing me issues is minimal. But... that risk is always there so be ready.
Anyway, that is what works for me. YMMV