If you have multiple warehouses, you set a fulfillment priority in your channel settings. You can have different settings for each channel.
Go to the Channel> Channel settings> Common and click Warehouse tab. You can select one of the options below from the dropdown menu of Fulfillment Priority Method;
Cost: If you select cost, the system will check the minimum product cost in each of your warehouses for the ordered item and the order will be completed from the warehouse with the lowest product cost.
Sort Order: You may sort and arrange your warehouse by holding and dragging up or down after selecting them. After you have reordered your warehouse, StoreAutomator will check the first warehouse on the selected list. If the ordered item is not in this warehouse, it will look at it at the second warehouse and will keep looking until the system finds the item in one of the warehouses. It won't check the third warehouse on the list if it is discovered in the second warehouse.
Distribute Order: It distributes the orders to the warehouses so each warehouse gets the orders. Basically, the system will apportion the orders out of the warehouses.