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.