any ideas??? i tried alphabetically but idk about that? any help would be appreciated.
Depends on what you’re storing.
If it’s mainly stones and such, I’d either organize by hue (blueish, greenish, etc) or if you’re really picky, by the index number for the color (you can see 'em all in the inventory → outfits tint window for quick reference in-game).
For other stuff, I usually do thematic shelves. One for metals, one for organics (creature drops and food), one for gear, one near the door for quick emptying of inventory, and so forth, with my preferred shelves being 18 storage boxes 3 wide and 6 high, per shelf, like so:
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I do it similar to @Arkhainn. I’m not sure if you have noticed but no matter how much blocks you stack only 3x3 can be accessed at once, that is the UI limitation. So it’s natural to combine 3 wide groups.
In one 3x3 I store creature and plant drops, in another soils, gravels, sands and other stuff I won’t use often, in another crafting mats and crafted items and in last one rocks. For now I’m getting by with foir 3x3 groups.
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Doing it like Arkhainn too. Organics, non organic, raw blocks (rocks, woods, ash/tangle etc, step 2 blocks (timber, stones etc), and step 3 blocks (refined and decorative go together for me).
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I have my storage right above my machines and store items according to what machine uses them the most.
I also try to build 3x3 boxes so that the storage interface shows all items at once when i open the middle box.
I’m working on a separate storage for colored wood and stone right now, as they don’t really fit in that system. 
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I do 3 height, and as wide as it fits me storage shelves. Rocks (stones, refined etc), wood, soil ones are I think 12 blocks wide. Organics (fungi, leafs, creature drops etc) are 12 wide too. Same with ores gems, and rest that is “gathered” with hammer, but in this case I think 12 is not enough, or I will have to move processed stuff, like machined silver somewhere.
Next time I’ll be doing this will make it 4 storage boxes when it comes to heigh, at least 4, but maybe 6, and 6 long at least and at most. To have it all nicely next to each other (raw ore, bars, alloys, compacted, refined and machined as an example)
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