Not sure if this has been resolved but what I did is this - (after download)
link the payment to the vendor
locate the check in the vendor center (open it up)
on the expenses tab use the account and use your a/p account
where customer job would be it will say vendor instead, use the vendor (this will change into "credit" sorta)
save it.
go to the bill
select pay bill
then use the credit available.
