Hey Sevenodd,
It's great that you've noticed this. Making sure everything is set up correctly only takes a small amount of time, and helps us produce accurate reports and forms. You seem to have a solid understanding of how this meant to be recorded, so I'm confident we'll have no problem setting this up.
In order to make a selection between net pat and gross pay, please ensure you uncheck each Payroll Item in the Taxes page. Checking items here indicates that this addition needs to be used to calculate net pay, so the system will default to gross.
Let me know if this works!