Eric, Most of affiliate systems require to put commission javascript code into thanks page, if this is the case for JROX JAM affiliate system then you have to put that code to /amember/application/default/views/thanks.phtml template.
In 3.x there was a plugin to generate the user in JAM and also a postback URL in the paypal plugin to notfiy of the billings. I dont think 4.x has this yet? David
Yes there is no such plugin yet. So if someone is interested in such plugin development, feel free to contact helpdesk.