Once you have your retainers set up its easy to maintain.

Eg.
Retainer 1 - Botany, Gardening and Chocobo items
Retainer 2 - Mining/metals/minerals
Retainer 3 - weaver, leather items
Retainer 4 - Gear

etc.

My wish is that we had a 'stack all' button, you can just hit it once and anything you are carrying that your opened retainer also has, transfers (stacks) onto the retainer immediately.

Throw out everything that NPCs sell for cheap.
Also anything that can be gathered very easily and isn't used very often for crafts.
If you have 60 NQ and 3 HQ of an item, either sell the HQ or reduce it to NQ and stack it.