Your set-up needs to match your procedural business flow so Atrex may be correct and you just need to think about how you do business further. Particularly, the question is how your warehouse fits into your supply chain as the warehouse could be your point-of-purchase (i.e., vendor - warehouse - store) or it could be an overstock location (i.e., vendor-store-warehouse).
In either situation, you should only generate a PO from either the store or the warehouse and only after attempting to resolve any shortage through a transfer.
In the first situation, the reorder report for the store gives you the amount to transfer from the warehouse and once the transfer is complete, you generate a PO from the warehouse based on the inventory levels you have set for the warehouse.
In the second situation, the minimum and target quantities for the warehouse are never considered and the store's target quantity must include the overstock amount you want to transfer to the warehouse once it is received. To determine what to transfer from the warehouse, you could use a sales summary report on a daily or weekly basis to indicate the quantities that need replenishing at the store. A custom report would be easier at it can be created to list only those stock codes that have quantity at the warehouse and the output from the report can then be used to directly create a transfer using the Load from File function.
Using multiple locations does introduce greater complexity and depending on requirements, you may be able to work with a single location. As with the second situation, a sales summary report will let you know what inventory to move from the warehouse to the store as it is consumed so that there is always an on hand quantity in the store.