My floss is stored in small baggies (like these) with each color in it's own bag. The bags are in a couple of totes and are organized by brand-> floss line-> color id.
Fabrics are stored in a large tote and sorted by type and size.
WIPs are stored in individual bags and/or pencil boxes if they will fit. If they are in the 'active rotation' group the floss is stored on binder rings with the project. If the project is in time out or I'm otherwise not planning on working on it soonish the floss goes back into the regular floss storage. I occasionally go through and purge WIPs that I'm no longer interested in because life is too short to spend your hobby time working on something you no longer want to make.
I use the Thread Organizer app to keep track of what floss and cross stitch fabrics I have, which colors are with what project, and make shopping lists as needed.
These small bags: Beadaholique 2 by 3-Inch 100 Self... https://www.amazon.com/dp/B009LIOMPQ?ref=ppx_pop_mob_ap_share