The system is designed to be able to receive partial POs. 

From the PO record, press the blue 'Receive PO' button at the bottom right of the PO.  This will create a Vendor Shipment recieving document for the selected PO.

Then confirm the items received in the first Vendor Shipment. 

If its a partial shipment of a PO (i.e. not all items on the PO were sent by the vendor), the PO will remain Open.  On the open PO, lines with all items received will be marked as 'Closed' and lines not fully received will be remain active with the line also displaying the items the items received vs ordered.

If you will never be shipped the missing items from the PO (e.g. if the item was discontinued by the vendor), you can select the line and mark it as 'Cancelled/Closed' using the action menu. This will allow the PO to be marked Closed.

It you are subsequently shipped the items by the vendor, you would click the blue 'Receive PO' button on the PO, which will create a second Vendor Shipment including all the items not received on the first PO.

You would then count/confirm the items on the second Vendor Shipment.  
If all items are receieved in the second vendor shipment, the PO will automatically be marked as Closed.