Collect a bunch of different mini-bags to put inside your backpack. The cheapest option is just use plastic bags from different stores and organize your stuff into specific bags, e.g. hygiene in the Walmart bag, food in the 7-11 bag etc. But even better than plastic bags in different colors is to get bags with slightly different material and shape so that you can shove your hand into your backpack and feel around in the dark and figure out which bag is which by sense of touch. So having, like, a nylon bag with a zipper, a nylon bag with a drawstring, a canvas bag etc. Just keep in mind that each additional bag that you are only carrying for purpose of organizing your pack adds more overall weight, so don't go crazy with bags-inside-bags-inside-bags.
Oh, and if you are shoving your hand into your backpack in the dark, make really damn sure that anything sharp you have in there is properly sheathed. Nothing sucks more than stabbing yourself with your own knife when you were digging round for a snack.
