With the new Amazon Selling Partner API, we are no longer able to add new SKUs to existing shipments. The quantity of existing SKUs in a shipment may be adjusted, but new SKUs will be added to a new shipment(s) even if destined for the same fulfillment center.

Once you have finished adding all of your items to a batch (Adding Items to Batches in PREP & SHIP) and (if necessary) listings have been created (Creating Listings in PREP & SHIP), then select the "Create Shipment" button or the "Create Case Shipment Plan" in the lower corner of the screen. 

Be sure the desired PO or batch is selected, as illustrate here: 

You should receive a shipment plan like this: 

When you accept the shipment plan by clicking the OK button, items will be added to the shipment(s) as outlined in the plan. You will see a green notification as well as the new shipments added to existing shipments in the Shipments column.