Hi Yaz,
First consider all boxes as Pallet.
Then if all these are related to one material activate Storage Unit Management for each storage Type.
Once you are activated SU for Storage Type, each time when warehouse movement will happen it will update with different QUANT. You can track all stock through SU.
If you storage location is Handling Unit managed, then configure HU. Once you are configured HU, you can manage all three boxes will with three different unique number identification with 18 digits (E128 is more recommendable). Also System will consider SU=HU
The configuration of HU details you can find in SCM660.
Hope this clarifies your issue.
Thanks in advance.
Ravindra Joshi