I meant to post the final resolution and never did, sorry about that... it occured to me, since you are running your site as a virtual all portals will have to have an alias of /dnn. So, once I added that alias to the existing list, it started working.

To manually change the order of the aliases is a bit tricky but can be done. First you must have at least two portals (which you did).

Let's say in this example that I have two portals that I want two swap the alias's around:

Portal 1:
mysite.com/portal01
mysite.com

Portal 2:
mysite.com/portal02
mysite2.com

Log into Portal 1 as host, go to Host | Portals

Now edit the alias's for Portal 2. Change the first entry to mysite2.com/ (leave the / so that it won't be identical to the second entry).  Change the Second entry to mysite.com/portal02. Now go back and remove the / of the end and you have them swapped around

Now login to Portal 2 and goto Host | Portals and repeat the process on Portal 1

Now you aliases will look like:

Portal 1:
mysite.com
mysite.com/portal01

Portal 2:
mysite2.com
mysite.com/portal02

And the primary site will be first.

As far as root installs, I know they don't support it, but they don't really support DNN or any custom website anyway if you get right down to it. That is up to you. Here is how I recommend setting up root web installs:

1. start clean
2. Create your database
3. Create the following directories/permissions:
   
   
   1. /App_Code                  Read - Write
   2. /bin                                Read - Write
   3. /Config                          Read - Write
   4. /DesktopModules       Read - Write - Web
   5. /Images                        Read - Write
   6. /Install                           Read - Write - Web
   7. /Portals                         Read - Write - Web 
4. WAIT for these to complete! The "pending setup" will go away. This is a very important step.
5. Setup you web.config file the same way
6. Make use SiteUrls.config is in the root - because the system will not have write access to copy it there
7. Using an FTP program like WS_FTP not Windows Explorer/Internet Explorer, upload the files. IE will over-write the permissions, you do not want that.
8. Then launch the install: http://www.yoursitename.com/install/install.aspx?mode=install

If you don't want to blow your DB away you could probably start at step 3 (Create the following directories/permissions), however, I'd FTP your site down to your local system, then FTP it back up to the root level according to the setups. That way, you have an EXACT copy of what is currently deployed. There may be some DB references to /dnn though, you will still have to leave that locatioin there for a bit until you clean those entries up.

I'm working on a fully detailed tutorial for this, however, it is not ready yet. this is basic information needed and you know how the GoDaddy system works to create the directorys, so I think you should be able to fill in the blanks. If not, please just ask.

what did you modify? what were you trying to do?

By the wasy I tried adding a parent portal and it dosent work at all.