There is actually two ways to do this: The first is a command line switch as you mentioned, and the second is a script command.
You can select a machine configuration via a command line option by editing the NCPlot shortcut. Right click the shortcut and select properties. The shortcut target string normally looks something like this:
"C:\Program Files (x86)\NCPlot v2.23\NCPlot.exe"
To specifiy a configuration, add the switch "config" to it like this:
"C:\Program Files (x86)\NCPlot v2.23\NCPlot.exe" config="mill"
You can create multiple shortcuts this way each starting NCPlot with a different configuration.
Another way to automatically select a configuration is to add a script command to the beginning of your programs:
(## NCPLOT.NCPSETCONFIG "MILL")
If you add this line to your program before any program commands then NCPlot will execute this as a script command, allowing you to set the configuration per program. The script command is executed once each time the file is loaded. This method actually allows you to execute ANY script command on file load, and there can be more than one line. Any line that starts with "(## " is treated as a script command as long as it appears before any G-Codes.