I am trying to install DNN 4.09 at DiscountASP in a Windows 2003/IIS6/SQL2005 environment.

I have an existing application using the root directory and the database that I do not want to risk while implementing DotNetNuke.  The following is a desription of the process DiscountASP described for installing DotNetNuke.  Please bear with me for a minute because I think those who understand the implemented architecture of DotNetNuke will be able to see my problem even if they don't follow all the details of DiscountASP's installation process.

DiscountASP's instructions (which they say are for version 4.04), call for:

1. dowloading DNN 4.09 Install to my local machine
2. setting up a subdirectory under the root directory
3. modifying the web.config file (2 changes to <connectionStrings> section  and <appSettings> section)
4. uploading the zip file contents into that directory
5. Configure IIS
   1. In IIS, make sure the ASP.NET Version is 2.0
   2. In IIS, make sure the Default document list includes Default.aspx
6. Set Up a Web Application
   1. Make sure you have Anonymous ASPNet ser and IUSR and that they have a quota of 200MB each.
   2. Open the Web Application Tool and navigate to the directory where you uploaded the unzipped DNN files to and click "Install Application"
7. Install DotNetNuke
   1. Open your browser and run http://www.YourDomainName.com/DotNetNuke_Subdirectory

When I did this, it looked like it was running.  I let it run for several hours (it said it could take some time and not to interrupt).  Eventually I had to stop it.  I tried opening that directory in my browser and it failted.
I checked my database and saw that almost 28MB of database space had been additionally used.
I had varied from DiscountASP's install instructions as follows:

1. As described in DotNetNuke's installation guide, I created a subdirectory under my Root Directory at DiscountASP. I then created another subdirectory under that one called "WebSite" and I uploaded the DNN files (with the modified web.config) to that directory.  (Because DotNetNuke's installation guide made a point that this was a new change to the installation process.) 
2. When it came time to install my application, I installed the directory 2 levels down from my root directory.

I then went to the directory that is between my root directory and the directory where I uploaded the files and also installed that as an appllication and tried again and that did not work.  I tried several combinations but was not successful.
Finally, I went back and reran the original browser command and the install program started again as an update.
When I went to http://www.MyDomainName.com/dotnetnuke_2/website/default.aspx, I get back the message that Domain name www.myDomainName.com/dotnetnuke_2/website does not exist in the database.

I am suspecting that I should have installed dotnetnuke exactly one directory down from the root as described.  But I don't want to risk that the install process writes anything to my root directory that could harm the application already running.

I am not sure what to do now.  My database is now full of a lot of DNN tables.  Can I just modify some data in the database to get it to recognize my application?  If not, can I simply rerun the install and will it "fix" whatever needs fixing?  Do I need to move the DNN files to the DotNetNuke_2 directory and run everything from there?
Is there anywhere I can find a brief overview of the architecture of DNN with regard to the tables and directory structure involved, especially if one has multiple portals?

Thanks in advance for any assistance.