AffiliateWP provides a filter for that.
This members-only tutorial provides the steps on how to add a directory inside a custom functionality plugin to the list of paths that AffiliateWP checks for overriding its templates.
Note: It is better/easier and recommended to use actions and filter hooks where possible to customize plugins' output where possible. Template overriding should be the last resort.
Install and activate My Custom Functionality plugin.
Connect to your hosting account using a FTP client and navigate to site's
Create a directory named say,
affiliatewp where you would like to copy the templates from the plugin to, for customizations.
Inside the plugin's
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