The WIX installer tool creates a way to manage this - you would define them as a part of the installation build instructions. It make some work to get all of the project configured but after that maintenance should be a breeze... Here is an excerpt from the Tutorial on creating the Virtual Directory entries...
6.3 Web Directory
The WiX toolset has additional libraries that allow the installer to perform additional tasks like creating a web directory in IIS. To use these extensions, all you have to do is to link against the appropriate WiX library. The linker will include the necessary helper DLLs into the installation package automatically.
First, we have to create the web site with the files belonging to it:
<Directory Id='TARGETDIR' Name='SourceDir'>
<Directory Id='ProgramFilesFolder' Name='PFiles'>
<Directory Id='InstallDir' Name='Acme'>
<Component Id='default.phpComponent' Guid='YOURGUID-5314-4689-83CA-9DB5C04D5742'>
<File Id='default.htmFile' Name='default.htm' LongName='default.htm' KeyPath='yes'
DiskId='1' Source='default.htm' />
</Component>
</Directory>
</Directory>
The next step is to create the virtual directory:
<Component Id='TestWebVirtualDirComponent' Guid='YOURGUID-6304-410E-A808-E3585379EADB'>
<WebVirtualDir Id='TestWebVirtualDir' Alias='Test' Directory='InstallDir' WebSite='DefaultWebSite'>
<WebApplication Id='TestWebApplication' Name='Test' />
</WebVirtualDir>
</Component>
</Directory>
Finally, create an entry to reference the web site:
<WebSite Id='DefaultWebSite' Description='Default Web Site'>
<WebAddress Id='AllUnassigned' Port='80' />
</WebSite>