You’ll want to use open display cases like bookshelves, metal racks, or counters unless you don’t care and just throw everything into a massive pile on the floor.
I have three different locations for different fields of crafting: the kitchen, the dorms, and the toolshed. built a 3x3 toolshed in my base, and then put a metal rack into every corner. If you label each space like you would on the numpad:
1: Containers (flasks, jars, bottles, canteens)
3: Items for disassembly (flashlights, useless CBMs, teleportation pads, etc.)
6: Metal (scrap, chunks, lumps, frames, plating,)
7: Electronic components (RAM, Processor Boards, copper wire)
8: Tools (Hammer, Wrench, charcoal forge/kiln)
9: Nonmechanical components (plastic bags, wire, string, blades, spikes)
The kitchen is arranged more meticulously. Once again, metal racks are used, and there is a row of five metal racks on the left side, and one on the right next to the solar-powered kitchen unit. Raw meat is hunted fresh, never stored, and there is an ample supply of wolf spiders, moose, bears, and rabbits outside the fortress walls.
Rack 1: Raw foods & Components (Bleach, Ammonia, spaghetti, mac & cheese, pesto, red sauce, flour)
Rack 2: Alcohols & Non-water drinks used in crafts
Rack 3: Completed, non-perishable foods not used in crafts (far enough away they aren’t checked for in the crafting window)
Rack 4: Purified water-filled canteens and bottles (For excursions out into post-apocalyptia)
Rack 5: Empty bottles
Rack 6 (To the right of the kitchen unit): Bones
In the kitchen is where I also store the seeds used in farming, as well as chitin powder, bonemeal, and plant food, on a counter next to the door.
The crafting materials used in clothe making are kept in the bedroom in four separate racks (Fur, rags, chitin, leather). I tend to keep a sewing kit on me at all times, with plant fiber/sinew/thread kept elsewhere for the sake of organization and keeping nothing on the floor. Clothes and armor have their own dressers on the other end of the room, and the clothes that have been scavenged have been repaired to reinforced status.
The armory has a series of metal racks for firearms, ammo, explosives, melee weapons, UPSes, and ammo crafting materials.
Wood is also kept in a separate spot on the base for construction purposes. Most of it is in the form of logs, which can be chopped into 2x4s.
And finally the medicine box is in a special place on the base, where all the medicines, drugs, narcotics, and first aid kits are kept. The narcotics will eventually get their own box. Why do I have them? For trading purposes.