Once warehouses are set up you need to ensure that you're using the appropriate view to handle replenishment to the different warehouses.
To see your warehouse settings, navigate to Account > Settings > Warehouses.
When you have individual warehouses and a combined warehouse set up, you should use the combined warehouse view to handle replenishment. You will then see replenishment needs for all locations that feed into the combined warehouse.
Note that you will need to set lead time and days of stock for your combined warehouse. A new warehouse will default to 14 days lead and 30 days of stock.
Keep in mind that the lead time for your combined warehouse will cover the time it takes from placing a PO with your supplier to receiving that shipment. If you need to send part of that shipment from one warehouse to another, you should include the time it takes to complete the transfer in the lead time.