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Go to Settings & tools > All settings & tools and under section Analytics & 3rd Party Scripts go to Custom Scripts. Click the Add New button to create a new script which you can name for example Post Affiliate Pro.
In the Scripts part go to Page Footer tab and insert the click tracking code there which you can get from Tools >Integration >Clicks tracking section of your Post Affiliate Pro merchant panel.
Switch to Purchase Confirmation (Thank You Page) tab and add the following sale tracking code:
Save the script and you are done.
It is now integrated. Every time customer enters the order confirmation page, the tracking code is called and registers a sale for the referring affiliate.