I want to avoid domain issues at GoDaddy in my Deluxe Hosting IIS6 account there.   I have 2 options for configuring new domains.

(1) I can add domains (to my hosting account) through Go daddy’s Hosting Control Center>Domains.   Each will exist as a folder off of my original root.  GoDaddy points to this method.     OR

(2) I can add and serve additional domains through my DNN installation.

A.  If I use option #1, will I have limited or no access to DNN from the additional domains?  AND will the single instance of MS-SQL be sufficient for additional fresh installations? 
B. Should I avoid the GoDaddy Hosting Control Center>Domain Set Up altogether and do all through DNN?

If you are familiar with serving multiple portals/domains @ GoDaddy, Many Thanks for your response.

You will need a little of both worlds to accomplish what you want. Let's say you have domain-1.com and you want to add domain-2.com. In your GoDaddy control panel you will go to Settings >> Domain Management, Add a Domain, and point it to the root. Now in DNN you will add your new portal and use domain-2.com/dnnPortalFolder as your alias.

A trick I like to use to get rid of the portal folder alias in the URL is this:

1. Create a throw away domain and use it as the hosting account domain
2. Point my real domain to a folder of the hosting account
3. Point all subsequent domains to that same folder
4. In DNN, just add the portals and use the new domain names as the alias