expense deducted from payment

You would most likely need to run the 2 transactions (receive payment and pay bill) through a clearing account. The clearing account is always a bank type account. Receive payment for the whole invoice amount and deposit it into this "bank" account. Then pay the bill but write the bill-payment out of the same clearing account. Now you have a balance in this account that should match the amount of the actual payment received. Make a deposit into your regular bank account and under From Account use the clearing account. Or record a Transfer from the clearing to the regular bank account. If you deposited this particular payment with other payments received as one deposit, you should add a line to the other deposit for this amount (From Account = the clearing account).

Reka