Hello there, kiowba. Thank you for posting in the Community forum.
In QuickBooks Self-Employed, there will be no Pay now button option when sending an invoice to your customers. You can let them pay the invoice using a bank transfer or any activity where they can pay outside the product.
Then, you can manually record the amount you've received by following the steps below:
Go to Invoice on the left panel.
Locate your customer invoice. If you want to record their bank account number where the payment was made, you can select the Edit option by clicking the drop-down arrow under the Action column.
Enter the account number in the Note to customer field. Then, save it again to reflect the changes.
Once done, select Mark as paid by going back to the selection in the drop-down arrow.