Some merchants run their own (in-house) affiliate programs using dedicated software, while others use third-party intermediaries to track traffic or sales that are referred from affiliates. There are two different types of affiliate management methods used by merchants: standalone software or hosted services, typically called affiliate networks. Payouts to affiliates or publishers can be made by the networks on behalf of the merchant, by the network, consolidated across all merchants where the publisher has a relationship with and earned commissions or directly by the merchant itself.
If you have pop-ups and optins on every page, I would have to think that it would be a lot harder to convince someone to link to it. Especially since the pages where you have your optins (and probably receive the most traffic) are probably the same pages that you have your best content on as well that you'd be hoping to pitch in your outreach campaign.