User certificates were created from Window's Server Cert Authority - we obtain user certs this way https://domaincontroller/certsrv since that is where our certificate authority is as the moment. If you are logged in with the user then they just simply walk through the process and it add's it to their machine.
I'm not sure I understand the Gateway cert question, we generated a third party cert and specified both in the portal / gateway this cert for our server cert. I also had to use our internal root cert to handle the user cert authentication.
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