There is no difference in trying to rank an affiliate site vs ranking any other site. You just need to do good solid practices and gather backlinks without spamming and using shady methods...its a long hard process...but worth it in the end of you do it right.

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Yeah, You will probably do the proper SEO for you affiliate website. You should use authentic ways to promote your website. Like use perfect keywords, quality content and generate back links from qualitative websites.

Yes, the keywords are going to different but the same methodology of SEO should be followed. Do your proper keyword research and use them across your site.