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