Sort your items using the Automatic Chest Sorter.
The chest sorting system works using storage minecarts and is able to move entire inventories instantly.
A very basic example of a chest sorting setup.
The storage cart can be put into one of three modes by having the cart pass over a powered activator rail with a wool block under it.
The color of the wool will change the mode of the minecart.
There are other settings that you can use:
Take Conditions:
Put Conditions:
Once you have configured the cart using the wool blocks, when the cart passes over a powered activator rail it will scan for nearby chests (2 blocks up, 2 blocks down, 1 block east, west, north, & south) and will put or take items as you have configured it.