How to Capture Multiple Payments for Multiple Shipments

A customer ordered from the site, and we only had part of the order on hand, so we shipped only part of the order, selecting the amount that we were sending on the shipping screen, then created an invoice and received the money for the items on the first shipment. Now we have the additional items ready to ship, and created a second shipment, but the site says that the invoice (which it has updated to include the amount that we’re shipping in the second shipment) has all been paid, even though we only captured payment for the first shipment. Is there a way to capture payment for the remaining amount?