When doing the transfers, if you create a Transfer Out, it will immediately remove the inventory from the stock of the sending location. The receiving location will have to create a Transfer In on their end to add the inventory to their stock. When creating the Transfer In, there are fields at the top right corner of the form to enter the store number it came from, along with the transfer number. This will allow you to have record of which Transfer In goes with which Transfer Out, and have verification at both ends that the correct items were received.
Alternately, if you instead create the transfer from the sending location as Transfer Out and In, it will take care of both steps. The inventory quantity will immediately be removed from that location’s stock, and as soon as the daily batch process is run, the receiving location will see it added to their stock. This saves a step of paperwork, but does not allow the receiving store to verify what was received before it is updated in their system.