Using GoDaddy's DNN auto-installation feature saves time and headache, but the installed version is still 04.09.00.  Well here's the lowdown on upgrading from the auto-installed version to the latest 04.09.05 version...
 
GoDaddy Auto-Installation
In a previous post I showed how installing DNN on GoDaddy is relatively painless if you use GoDaddy's auto-installer and also make a few configuration tweaks (to get rid of the installation directory name in your site's URLs).  That process is what I now use for clients who chose to host with GoDaddy and it works well.

Unfortunately GoDaddy's auto-installer uses DNN 04.09.00.  What if you prefer the latest 4.x version (currently 04.09.05)?  What if you wish to move up to DNN 5.x (currently 05.01.02)?
 
The short answer is: it's pretty easy to upgrade an auto-installed copy of DNN. It's not as easy as using the auto-installer, but it's a bit easier than installing DNN in GoDaddy's root folder (as many people seem to think you have to do...but you usually don't).

Upgrade Steps
In a nutshell:

1. Use the GoDaddy admin dashboard to make a database backup (just in case!).
2. Use your favorite FTP program to download a copy of your website files to your local computer (just in case!).
3. Unzip the "install" version of DNN 04.09.05 on your local computer and make needed edits to the new WEB.CONFIG file (more on this, below).
4. Use your FTP program to upload the whole "install" version of 04.09.05 to your GoDaddy website (right on top of the old files) along with the new WEB.CONFIG file.
5. Open your website and watch it upgrade itself (takes less than a minute). Done!

The only hard part about this is waiting for the FTP transfers to complete (there are more than 3000 files involved).  My FTP transfers typically require between 10 to 20 minutes for a standard DNN site.
 
 
Details
 
Step 1: Database Backup
You'll need to know your GoDaddy management account name and password in order to use the management dashboard.  Log in, select "Hosting" and then the "Manage Account" link next to your website URL.  In the new window, select DATABASES, then your DNN site's database and finally the "Backup" option.  You'll be told where the backup file will be stored -- make a note of it.  You don't need to do anything with the file other than know where it is in case things go wrong and you need to do a database restore (hasn't happened to me, yet).  The backup should finish in well under an hour for most DNN sites so by the time you're done with steps 2,3 and 4 the DB backup should be complete.

 
Step 2: Files Backup
You'll need to know your domain account name and password.  This may or may not be the same as your GoDaddy account name/password.  The domain account name and password is when you'll need to access your files via FTP.
 
Yes, yes...I know GoDaddy provides a browser-based FTP interface through the dashboard but it is simply not sufficient for moving the number of files we need to move.  If you don't have a favorite FTP program already, go and get the great (and free!) Filezilla here.  I'll wait.
 
Done?  Good.  Now FTP into your website and copy the entire DNN installation to your local computer for safekeeping.  Your site's FTP address is "FTP.{domainname}".  That is, if your site is "abc.org" then your FTP address is "ftp.abc.org".  Simple, huh?
 
 
Step 3: New DNN files
Now you need to get the latest 4.x DNN version onto your GoDaddy account.  As of this writing the latest (and possibly last) 4.x is version 04.09.05. Get the "version upgrade" package of it here:

  DNN 4.9.5 - Version Upgrade

All the files in the "version upgrade" package are perfect the way they are except for one: WEB.CONFIG.  Actually there is no "WEB.CONFIG" but rather "RELEASE.CONFIG".  Rename this to "WEB.CONFIG" and then open for editing.  Also open your old "WEB.CONFIG" that you downloaded in Step 2.  You're going to copy a few things from the old file to the new one:

1. DB connection strings. 
   The GoDaddy WEB.CONFIG defines a connection string for "SQL Server 2005 Express".  Go ahead and copy the connection info (within section "connectionStrings") from the old WEB.CONFIG to the new one.
   
   Now, just below that section is section "appSettings".  The core BLOG module (among others) needs the DB connection info to appear here as well.  Again copy the relevant line from the old WEB.CONFIG to the new one.
    
2. Machine Key
   Muy importante!  If you don't copy over the old machine key then all of your existing DNN user passwords will cease to work.  Around line 90 is the "machineKey" tag.  Copy this entire line from the old WEB.CONFIG to the new one.
    
3. Old versions of DNN often included an "objectQualifier" value by default.  This value was used as a naming prefix for all DNN-related database objects.  In current DNN versions this value is blank by default.  You should not have to fool with this but, just to be safe, search the old and new "WEB.CONFIG" files for "objectQualifier" and make sure they match (they should both be blank).  If not, copy the value from the old file to the new file.
    
4. If you have previously altered ANY values in your old WEB.CONFIG prior to attempting this upgrade, you will need to find and copy those altered values from the old file to the new file.  A good tool for comparing the old and new files side-by-side (so you can esaily spot differences) is the free WinMerge compare utility.  Read about it here.

All done?  Save your new "WEB.CONIFG" and go on to step 4...
 

Step 4: Upload New DNN Files
Using your FTP program once again, upload the new DNN 04.09.05 files to your website.  The new files should go right over the old ones.  This is why we downloaded a backup copy of the old files in Step 2.
 

Step 5:  Cross Fingers
Your site is ready to upgrade itself!  Browse to any page on your site and the upgrade process should automatically kick off.  Within 60 seconds or so the process should complete.
 
 
Big Fat Disclaimer
This process works well for me but there are no guarantees that it will work in every situation and for every website.  If your upgrade attempt fails and you cannot rectify the issue, use the GoDaddy admin dashboard to restore your original database (from the backup file you created in Step 1) and use your FTP program to upload your original DNN files (that you copied down to your local machine in Step 2).
 
 
Upgrading to DNN versions 5+
A final word of caution:  When upgrading to a new version of DNN, always check the "recommended upgrade path" to make sure you're not upgrading too far in a single step (DNN doesn't like that).  DNN Corp recommends upgrading from version-to-version in order without skipping over any interim versions but that's quite tedious.  To save time, check the recommended upgrade path here to show you how many DNN versions you can jump per upgrade.
 

Good Luck!