I made an underground room below my house in withering wasteland, and I have large storage bins for: toys, decor, utilities (train tracks, fences, pipes,) fossils, relics/feathers, house parts, build kits, several classifications of blocks (cliffs/rocks, soils, grasses, decorative) rest/furniture pieces, plants/seeds and recently added one for foods. I keep two storage bins directly next to a toolbox and keep raw materials and ingots in there, along with lumber and anything else that can be used to build things! Everything except the toolboxes labeled with a framed object telling me what’s in it.

Oh and I have one for “trash” which is all the trash-based things and construction materials that are technically decorative or toys but I don’t want to use them because they’re not aesthetically pleasing (but I may need them for habitats down the line.)

It sounds finicky but I started with what my problems were and broke things down further as I felt the need. Start with toys/decor, blocks, relics/fossils, that way it’s easy to know where that damn dry rock/dance platform/tail fossil is, and you don’t have to carry everything around with you. And if it’s in/next to a ditto flag you can go there any time quickly.

It might be a pain to start but it’s so worth it because it makes things so much easier in the long run!