You can run an income report to see which invoices have been paid via BPAY.
To run a BPAY income report:
Click Reports > Finance.
Click New Report at the top-right of the page.
In the Report Type drop-down menu, select Income.
In the Payment Methods field, select BPAY Auto. (NOTE: "BPAY" is for payments you have manually marked as paid via BPAY, whereas "BPAY Auto" is for BPAY payments processed via Halaxy).
RESULT: An income report will be generated, showing invoices that have been paid via BPAY.