Great question — answering as the UphillTech team:
Google Analytics does require tagging to distinguish organic and paid traffic. If traffic does not have utm tags, then Google assumes that it is organic. If you have an affiliate parameter on the URL that is not a utm parameter, you can use JavaScript to inform Google Analytics about the campaign : ga('set', 'campaignName', 'Affiliates'); ga('set', 'campaignSource', 'Affiliate Bob'); ga('set', 'campaignMedium', 'paid'); ga('set', 'campaignContent', 'Ad by Bob');
Full answer by Stephen Ostermiller: https://webmasters.stackexchange.com/a/76175 (CC BY-SA 3.0).
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