I use both pre-made charm packs and I make charm squares out of my scrap stash when I need to feel productive. I don't separate the pre-made charm packs, and I don't really organize the ones I cut out.

I no longer buy charm packs or layer cakes, for many reasons already mentioned. I sold most of mine when I did a massive organizing binge and the ones I do have left are stored in a dresser. I keep everything by fabric line and don’t mix and mingle those. I do break up most of my fat quarter bundles since 90% are Batiks. Those are sorted by color into plastic bins.

I dont break any apart until i want to use them. Layer cakes are stood up like books, jelly rolls are on a small metal tall skinny shelf i got from IKEA (only because the shelf fit in a small space by end of cabinet and i wanted them all out so i could see what i have and start using!). As my room progresses i will do different things.