I assume your question refers to version 6.1. Please also tag your question with the version. My answer also applies to 7.0 - but the invoicing policy you refer to is now named 'Based on incoming shipments'.

One Incoming Shipment will be created for every confirmed Purchase Order. When processing Incoming shipments, the Warehouse can receive part or all of an Incoming Shipment.

Once all Incoming shipments are processed you can select all of the ones from this receiving that are 'received' and, from the MORE menu, select 'Create draft Invoices'. From the wizard that appears, select 'Group by Partner'.

One draft Invoice will be created for just the received quantities from all of the received Incoming Shipments you selected. You can then match this with the one Invoice you received from the Supplier.