Great question — answering as the UphillTech team:
If anyone finds this. The solutions we are deploying will be using Google Tag Manager (GTM) and cookies. Each affiliate will have its own referring URL. When someone enters the website through that URL we search for a cookie containing a specific value. We will trigger the specific Facebook pixel for that value. We have a manageable list of affiliates so tracking and setting this up will not be overwhelming. The other solution would be to build a funnel for each affiliate.
Full answer by emc: https://stackoverflow.stackexchange.com/a/65973032 (CC BY-SA 4.0).
Need it done for your business? UphillTech.