How do I turn this off so if affiliate #1 sends a user to my site, but the user does more research and ends up back on my page from affiliate #2, that #1 will still get the commission?
There is not such option in aMember. It require customization of core file You can alter this behavior in file amember/application/aff/controllers/GoController.php in method indexAction before setCookie check if cookie is already exits and do not set it again in this case.