Once you have sent your ABA File to the payment processor, be it a Payment Gateway, Bank or somewhere else, you should receive a response file with which payments were successfully processed and which were not processed.
You will need to update the Payment Batch lines to reflect these Successes and Fails. There are two ways to do this, a Bulk way and a line-by-line. You will need to Edit the Batch record.
Bulk Update:
There is a little Dropdown next to the Status column, which allows you to update all the lines to Success or Failed.
Line-By-Line:
Once you have bulk marked the majority of the lines to a status, you can manually update single lines to the other status. ie Majority of lines were processed successfully, but one line failed, you can adjust that single line status.
NB You will also have to update the Status of the Batch to "Closed" before you can save the Batch.
All Opportunities which were Successful will have their statuses changed to "Closed Won" and the PPayment Transaction status will be Success.
Failed Payments will show on the Opportunity as a Failed Payment Transaction, and the Stage of the Opportunity will remain at Prospecting, unless you have 3 failed Payment Transactions, in which case the Opportunity status will be updated to Closed Lost.