To save multiple NC Setups, first create and setup just like you need. But NC Setups will not save with FILE templates.
To save a template that will load with multiple NC Setups we need to highlight all of them then go to NC utilities- Template-save.
Then switch the file type to .mtt and save. 
Now go to TOOLS> PREFERENCES> GENERAL> GENERAL NC and check the box for "Auto-Load Default Template:".  Browse
to the previously save template and open. Save the new settings.
Now when opening a new NC file it will load with the NC Setups that were created for each file.