Elias here with Shopify Support. Thank you for reaching out!
I understand you’re looking to add a 3rd party affiliate program to your store. This is definitely possible; however, I’d need more details on the setup from your 3rd party affiliate program to make sure I am giving you the right information.
Typically an affiliate program uses a unique link, so they can track who’s website is referring the customer to their store. The unique link can be added to your navigation menu and customers can navigate that way. Alternatively, you can also use the sections on your homepage, which can let it seem more like an ad on your website.
Let me know if this clarifies your question? If you have any other questions on adding a 3rd party affiliate program, don’t hesitate to let me know in this thread!