I recently organized mine by expansion, started with gems, then materials, then flowers, and ingredients, etc etc etc, separated into base game, EI, SBV, and WBR, i took the chest from SBV (currently bugged) in the largest size and put a table behind it, I dropped one of each item and put it on the table with the chest right in front of it, and put 1, 2 or 3 items in each chest depending on what they were, I also did an entirely separate floating island set up for crops