>\Windows\System32\inetsrv\appcmd.exe set vdir "Default Web Site/MyAppName/" -physicalPath:"C:\MyAppPath"
For more information relating to appcmd.exe and it's various usages, see this link here...
Also to discover which app pool workerprocess is which you can use the following command
%systemroot%\system32\inetsrv\appcmd.exe list WP
or just look at your task manager with the command line column expanded for the w3wp.exe process