I needed to upgrade some other DNN sites so i Ioaded 05.06.03 onto another server to function as an upgrade machine.  unlike my earlier post, i loaded DNN at the root of the IIS website and created a couple of sites to test aliasing and it works fine.  on my production server, i pointed the webserver to the parent of my dnn folder.  I've done this before and it has worked before with pre DNN7 versions for GoDaddy shared virtual hosted DNN with multiple sites.

Ideally, a best practices document that describes how to correctly setup sites and aliases for both configurations would be very helpful.