9.0.2 and Windows Server 2008 R2 SP1

How should IIS be setup so ASPDNSF runs in the domain root and not from a directory?

After setting up ASPDNSF according to the manual for Win 2008, I navigated to the "Basic Setting" of the default web site in IIS and set the physical path to the "web" directory. I left the application pool on "DefaultAppPool" because when I change it to Classic .Net AppPool the site loses the correct file paths.

It seems to be working okay. Is this best practice?

Thanks!