Since you get to the deployment manifest via a Url, you can pass all of that information via the query string (e.g. http://clickonce.example.com/shell.application?p1=this&p2=that
)
I was going to type out the steps, then googled and found this blog that basically lists out all the steps. I've done something similar in one instance with no issues. The only slightly difficult thing is that you have to re-mage after setting things up, but if you got it to deploy in the first place, you already know how to set things up.
Good luck!
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