This is one feature that Volusion suports that works extremely well. Their implementation is quite simple. Every order has two totals, the total purchase amount and the total paid. If the customer enters a credit card at time of purchase, then the two amounts are the same. However, if the store creates a manual order and includes the PO number, the paid amount is zero. Then, when the store receives payment (could be check, direct deposti, etc, etc), the store's accounts receivable updates the order. You can even enter the check number and other transacton identifiers. It also allows partial payment. There is a simple report that shows all orders that have an oustanding amount due.
I have reviewed a number of ecommerce solutions, and this feature is missing from most of them.
