There is no layer order. You put things in order on the ‘+’ screen, and when a body part gets damaged, it checks the stuff from the bottom to the top, so if you want to protect something, put it near the top of the list. Full stop.
The layers (currently) do nothing but control encumbrance stacking. That is, worn clothing gives encumbrance, and when you wear two (or more) items on the same body part that have the same layer, there is additional encumbrance added beyond what they usually give. I don’t know the formula for it, sorry.
In theory, at some point, they might make layers matter for order, but it hasn’t happened yet.
In practice, I usually try to put things in the “right” order - close to skin, worn as clothing, waist, over other clothes, strapped. How do I know that’s the order?
Well, “close to skin” is obvious - think underwear. “worn as clothing” would be next, as that’s pants. “waist” would be belt - you put that on AFTER pants, yes? Next would be “over other clothes”, as that is coats and jackets. Last would be “strapped”, since that’s backpacks. Imagine putting that on in ANY other order, eh?
(OK, I have actually put a backpack on before a large coat in a very few circumstances. It does feel pretty weird, though. Smaller bags (lime a messenger bag) feel less weird, and I’ve seen women wear small purses under coats pretty regularly in cold weather, so there’s that.)