You can put them in an order that makes sense to you-- alphabetical or category seem to be the most popular.
Then figure out when your ads come out for the stores in your area. Come find the forums here for those stores and see if there are previews. Several stores have previews of a day or two, others have previews of two or three weeks.
Once you look over the preview ads, you can make a list, pull coupons, and then organize them in the way that make sense to you. I don't drag binders into the store, so the way I organize mine is by taking folded papers with each store's name on them and putting the coupons in them. I store them all in a pampers wipes box that I do
drag into each store.
Others use envelopes with the store names and dates of the sales on them, others take their whole binder in with just a dated list of what they want to get.
DELTA region for Kroger stores