To split the quantity of an item between more than one box in BoxT is easy. 

For items with a Quantity > 0, you will notice after scanning the first item that the system will automatically put the entire quantity into the same box.  If needed, you can transfer items into different boxes by clicking the item, changing the Quantity desired in that box and clicking TRANSFER.  The remaining Quantity will be transferred into another box.  If you need to split/transfer the Quantity even further you can do so.