Andy M.
Certified Pretend Chef
I do mine alphabetically. If the name is part of the spice (e.g. Red Pepper Flakes in your example), it would go under 'R'. If the name is not part of it (e.g. Crushed mint) it goes under 'M'. And then I store some on top of my spice rack because I ran out of room.
But after a few times you remember that Red Pepper Flakes is 'R', etc., no?
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Interesting. I took the opposite approach. All peppers are in the "P"s. Cayenne, red pepper flakes, paprika, etc. Whatever works, right?