Are there more detailed instructions that explain each step within the above autodomain -configure process??
you should find a manual along with the script which details all the options?
For example the 1st step in the -configure process asks for a "high level admin" user credential. IS this just for a 1-time step? OR will this login be hard coded into AutoDomain and we should use a dedicated account?
It's just for the configure process - it's going to create scripting users and groups for you etc. If you already have that though, you don't need to run the configure routine, just set the right options in the ini file to match your environment
The second step in the -configure process asks us to pick a name for a "special scripting account" that the configure process will create. Since we're already using AutoDomain 5.25 don't we already have one??
Yes you do - configure is only really used when you're setting up for the first time.