The server where I want to install my website has more than one 'root'
website in IIS - "Default web site" and another website. Both use port 80.

When Windows installer runs, it prompts the user only for the virtual
directory name and port number. It does not install the site under "Default
web site" but under the other web site (presumably, because the other site's
name starts with "a", and it finds this first). This despite the other
website being inactive.

I want the website to be installed under "Default web site" (or
alternatively, in its own root), but I don't see any way of forcing this in
the .NET Web setup project or providing the user with a dialog to specify the
target web site.

I tried altering the setting of the Web application folder's IsApplication
property (which specifies whether an IIS root will be created), but it
installed the web site in the same place as before.

Thanks in advance for any suggestions.