In this update, we have made a change to the template which allows you to choose the ‘Calculate Bill By’ field to either:

Margin %  / Markup % / Profit / Bill

To do this, go to:
Settings > Admin Settings > 1. Organizational Settings > Compensation Page > Pay & Bill Templates  > 'Create New Template
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Depending on which you choose, you will then be able to apply the relevant percentage or amount required:
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For our Australian customers, you now have the option to include/exclude Super in Pay: