If you want to transfer, for example, 100 unequiped augs to storage from a main ship, then Transfer Type option wont allow you to do it. It says : Nothing valid or unequipped to transfer.

At the moment, as far as I understand, It counts Equiped augs and as a result to transfer can be made.

Thanks

Apparently if you ctrl + click them or Shift + click them then transfer using the transfer command on the dropbox, you can then transfer them between ships.