Log into the backend of Magento and go to Sales>Orders.
Find the affected order and click on it to go inside that order.
Click on Invoice in the top right hand corner of the screen and then click on Submit Invoice at the bottom of the subsequent screen.
The order status will remain the same but the order will now have a paid invoice attached to it.
Log into Print Manager and search for the order by print job ID.
Mark the order as paid in Print Manager.
Click the Edit button and manually enter the name, address, order number etc. into the relevant fields.
After a short delay (about 20 mins) the order should then be ready to process.