Hi,
It looks like you're on the right track!
The registerCommand() function calls take the command string and the name of the command. So in the case of ApplicationFacade.as from the best practices guide, there needs to be three command classes: StartupCommand, LoginCommand, and GetPrefsCommand. You would create these in your controller(s) directory.
There are a few helpful demo applications that you might want to look at: Application Skeleton (AppSkeleton) is nice for showing how to setup directories & files. EmployeeAdmin is from the courseware (I think) that is often mentioned around here. That's a really helpful example for showing how everything works together.