I've stared by sorting items into a few categories. Craftung, Building, Smithing, Farming etc. I've also build multible buildings designated for different tasks. Like a bakery, a smithery, a farming hut etc. For items like copper nuggets or so I tend to use crates since they hold only one item. The rest is kinda thrown into whichever storage vessel it seems to fit regarding my categories. Copper bars/Iron bars etc. I keep close to my anvil in case I need them.
Hope i could lend you and hand by that ^^
Cheers, Yama