Dynamics GP 2013 includes new functionality that allows you to create prepayments in accounts payable and assign them to specific purchase orders. You can easily do this from the Purchase Order Entry screen. You can enter a prepayment amount that you can then generate a check for using the regular computer check functionality in GP. Or you can create a manual check transaction that is associated with the purchase order.
Lorna Link at InterDyn BMI covers this topic in much more depth at the ERP Software blog, here: http://www.erpsoftwareblog.com/2012/10/gp-2013-new-feature-purchase-order-prepayments/
I created this short video to show this new functionality in action: http://youtu.be/RXB7-xmf_jo