If a line shares the same account, date and reference, the software groups them together. To separate the lines for recording payments, use different references.
You can record any payments you've already received against batch invoices:
Amount paid
If you want to record the payment at the same time, enter the amount paid.
Pay Date
Enter the date of receipt.
Bank A/C
Your default bank account appears. If you need to change this, click the arrow then double-click the required bank account.
Pay Ref
Enter a reference for the payment.
Check your batch totals are correct, then press Save then Close.