Hi promobility,
Please record the full amount received on the bill payment - this will create an unapplied payment on the supplier's account, and you can then follow the steps below to record:
1. Select + New > Bank Deposit, to show that the money went into your bank account
2. Choose the correct bank account on the top left corner, choose the date when the money actually hit your account
3. For Received from choose the supplier, for the account choose Creditors, enter the amount, choose no VAT
4. On the Supplier's page create cheque
5. Tick the bank deposit against the unapplied payment and save and close
6. Match the deposit against the transaction on your banking screen
Thanks!