I generally have a chest per item type. So one for seeds, one for fish, one for misc materials (clay, wood, stone, fibre), food stuffs, mining stuff (ore, gems etc), then in my 'big' game I have chests for gold quality items and iridium quality items (1 of each).
I'm converging on this design, spent some time yesterday moving things around and splitting out some generic "crops" chests into "fruit," "veg", and "forage/flowers." Additionally, I have small areas marked out with flooring eg. one where I have cheese presses / mayo machines / looms and a chest that stores the inputs and outputs of those processes. Although I mostly sell the outputs, and just keep a small stash.
I've done all the bundles now, I'm concentrating on iridium (I have a paltry four iridium sprinklers and only 2x tools upgraded) and friendships.
I really wish you could upgrade the fridge so that you could store all of the food in there.