I have used CMS system which has one installation [source code/database] and many websites. In IIS, I have created one website host.domain.com and created one virtual directory "CMS" which points to the my source code.
Now when I need to create a new website in my CMS application, I have two options either I create new website and vdir "CMS" in IIS which points to the source code or I can create host header of it on "host.domain.com" website. I
have chosen second option as I want to use same application pool for all my websites and whatever settings of IIS (like IIRF ISAPI filter, 404, etc) I do for host.domain.com will available for all host headers.
Now regarding sitemap, IN CMS application, Sitemap is created based on the URL(website URL) and for that I have created one .aspx page which returns sitemap [XML format].
Eample of sitemap URL that google will request is
(1) http://one.domain.com/sitemap.xml?Page=1. Now this needs to be rewritten to http://one.domain.com/cms/sitemap.aspx?Page=1
(2) http://second.domain.com/sitemap.xml?Page=1. Now this needs to be rewritten to http://second.domain.com/cms/sitemap.aspx?Page=1
For above rewritten I have installed IIRF on host.domain.com website and added below rule in website IIRf.ini file.