When making an actual payment, select the Bill Clearing account as the BANK ACCOUNT instead of your normal transactional account.
Then go into Banking - New Batch
Type - Withdrawal
Bank account - your transactional account
Clearing account - Bill Payment Clearing
Add a reference
Click 'add batch'
Click EDIT selection and choose the payments to add to the batch
Click Save then Confirm.
From here you can then download the .aba file to upload to your bank.
Here's is a HELP file which explains how to process a Batch Payments - https://login.shoebooks.com.au/net/pages/Help.aspx?from=Banking