If you have identified merchants for whom you think you could generate substantial revenue through an affiliate marketing relationship, there’s no reason not to attempt to set up a direct relationship. There’s also not much magic to pursuing this type of arrangement; if there isn’t a pre-existing relationship, start by reaching out to your potential partner and telling them a bit about your site.
When you have your own product or service you hold a lot more control of the funnel from beginning to end. But I’ve worked with many marketers to help them better control the best affiliate marketing funnel with banner ads, blog posts and social media. Once people move from those elements to the sales page – I help them control their message and email marketing campaigns and everything behind the scenes.