You can accomplish this by creating an "Import Order":

1) Open up the SMRT account of a customer with a balance to transfer
2) Click the New Order box; then click on the "Import Order" tab
3) Enter the amount of the balance from the old system in Price
4) Include a note like "Old System balance" or something similar in the Description box -- this description will show up on the Customer Statement
5) Click the blue box "Create" in the lower right hand corner
6) Then in the order pickup box on the right side click the green box with the corresponding order # (if the customer has no ready orders it'll be the only box there)

This balance will now be included on the customer's next statement or you can pay it now.