First, you have the option of planning each warehouse separately. On the storage dimension group 'Coverage plan by dimension' is ticked for the warehouse (sounds like this is the case in your system).
Then item coverage records define for each item in each warehouse whether you will get a transfer order or a purchase order. But there is a default on the warehouse itself. On the warehouse record, master planning fast tab, if you tick 'Refilling' that's a default transfer from the 'Main warehouse' unless you over-write the planning with an Item coverage record.
Finally on the Site there's a setting to use transfer journals instead of transfer orders.
Try creating some item coverage records - review and over-write the defaults and check the setup by updating master planning on the Net requirements form.
Hope this helps
Tim