GoAffPro provides you with the option to track affiliate referrals even when you are using a third-party theme in your store.
To track affiliate referrals when you are using a third-party theme on your store, go to the Advanced section of the Settings tab in the GoAffPro admin panel.
Go to the Third Party Tracking section.
Here, enable the toggle.
Now, copy the tracking code and embed it in the page where you want to track the affiliate's referrals.