The first thing you should do is to go get backpacks of different colors, you can buy them from NPCs on different cities, check this, some quests will give you special backpacks although you can have enough variety just from NPC Shops.
We use Backpacks since they have 20 vol. and while chests, gift boxes and other containers look cute, they're not practical and end up being a disturbance more than helping. Also, deeper levels of backpacks can be any color, except on certain
Organize them by what each color reminds you most of, here's how we organize our Depot: