This is how I have organized mine, because i have seen is the best way (in my opinion):
First you need to have the 'main backpack' (where you have all your stuff) inside of another backpack:

This way, when you use rings, amulets or create runes and amunition, they all gone to the first empty bp, making it easier to put them back to their right backpack.
Main backpack: I use a representative item before the backpack that contains those items:

*In the jelewey cases I have the dishes that heals mana and life (but I dont realy need to open them since I got them on the action bars and hotkeys).
If you want to maximize your capacity I would use theses backpack, depending of your economic posibilities:
1- Blossom backpacks
2- Backpacks of holding
3- Pillow backspacks
4- Festivity backpacks
5- Jeweled backpacks
About the loot backpack, I would use the ones I have already named. I loot everything in the same backpack, so when I go to the depot I just 'throw' the 'stackable items' in the 'stash' of the depot.

Hope I helped.