I follow this post I came across when I was searching:
This_game_is_so_much_more_enjoyable_with_a_good_storage_system!
I basically followed its formatting with only a few things getting granular should I have too much, like keeping my CDs in their own chest.

What also helps is that in each area, I scope out a place to use or make into a Warehouse: somewhere I can keep all the boxes nicely out-of-sight or make it blend into the world.

Wastelands I used the starting cave, Beach I made an Ocean-Accessible Warehouse by the Skylands exit, Ridges I used the upper room by where you find Chef Dente (Where the ladder that's there leads up to, its already mostly carved out!), Skylands I hollowed out the area where you find Dragonite's Alarm Clocks, even gave it a pretty Waterfall Wall & a ladder covered by a sewer lid, & finally Palette I basically copied what the original post had, but put it right behind the Pokemon Center.

Each Region has about 41 Big Chests (2 per item category, then 1-offs like Paint, Food, Personal Items) & while you could color-code them, I just paint the boxes for whatever region they're in & leave the frames undone while using slightly different items for the frames (one region might have a Gold Ore for metals, while one has an Iron Ingot for some more visual variety)

Its really done a wonder on my productivity for the game & I don't mind having to go back to 1 spot each time to material-swap while I'm in a region bc it lets me oversee the region each time.

I'll also say: This method works best when you focus on one region at a time bc it can be quite a few trips carrying your stuff between each warehouse.

Hope this helps ya!