Anyone use AdminStudio?

[oddyager]

Okay, I'm probably an idiot, but the .msi file I create from AdminStudio only has the customized config changes, correct, and not the actual exectuable program? How do I incorporate that into the .exe file so that when I run the executable it also installs the customized config settings? Do I need to import the .exe into the .msi? I used the wizard and it doesn't seem to do that.