Vendor’s prepayment in procurement process is a very common practice and in such scenario an organization should be able to track purchase order & their prepayments.
Earlier in Microsoft Dynamics AX 2009, it was not possible to make a prepayment related to a purchase order and these were always two separate manual processes. (There was no transaction link between the prepayment for a purchase order and the actual purchase order)
With Dynamics AX 2012 it has been made very easy & simple with prepayment functionality.
Vendor prepayment process is explained in detail by Sandeep Chaudhury on his blog in a detail article. Check it out HERE.