After you have authorised your ABA/Batch file payment in your pay.com.au account, you will be able to reconcile the payment typically the day after by following the steps below:
1. Log in to your Xero account
2. Locate the bank feed payments were made from, click on Reconcile items
3. Locate the debited transaction on the left, select Find & Match to locate the corresponding batch file
4. Click Adjustments > Bank fee
5. Fill in the Bank Fee transaction details as below:
Contact - pay.com.au
Description - Processing Fees
Account - 404 Bank Fees
Tax rate - GST on Expenses
Amount - Copy and paste the amount your balance is out by
6. Click Reconcile