Are you talking about changing the URL for the location of your ClickOnce deployment?
If you install it by calling the link to the application file itself, does it work? Is the problem the setup.exe file not looking in the right place?
If so, here's some excellent information:
Open a command window and change directories to your setup.exe file.
If you type in "setup.exe -?" it will show you the options.
To change the URL where it looks for the ClickOnce deployment, use -url.
setup.exe -url <new path to deployment manifest>
example:
setup.exe -url
http://www.mycompany.com/myappname/ RobinDotNet
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