I have 4 12 x 12 3-d scrapbooks (the cheap ones from HObby Lobby). They all 4 have about 40 protectors in them which is 80 pages with both sides.
I have all my words, diecuts, stickers (except letters - those are in a carrying case for crops) and flat things (not dimensional flowers) but flat flowers and even cardstock I've bought that is shaped around the edges in the books.
I take the white paper that is in the sleeves and tape the packages all over it.
The first book is "Bling" "Full Page die cuts" and "Flat Flowers" - the packages they come in are just taped there so I can pull them off. Some of the packages are bigger than they need to be and those are trimmed.
The next book is "Cat" "Animals" "zoo" "Hospital" "Sports/Games" "Pool" "Food/grill/restaurants" "Scrapbook/scissors" "Handyman/HOme Projects" and "Misc."
Book 3 is, "General Traveling" "USA by state" "International by Country" "Cruise" "Beach" Diving" "Aquariums/fish" "Lake"
The Last book is "Holiday" (starting with Valentine's Day, then St. Patricks, Easter, 4th of July, etc in order ending with New Year's Eve), "Birthday", "Babies/Children", "Engagement/wedding". Anything to do with love is under "Valentine's Day"
I just look on the spine of my scrapbooks to see which book they are in and then thumb through to find it.
I'm using a lot more of my diecuts, words, stickers and flat embellies since I orgainzed like this.