That is precisely how you do it.
The "template" tournament wouldn't be counted in the stats, because it isn't a completed tournament. Even if it were, you could still use the Filter to filter it out of your stats.
Better than loading that template tournament when you start, just set it as the "default" tournament. On the Preferences tab, press the Config Files button and set your default tournament to your "template" tournament file.
Once your default tournament is set, the Tournament Director will load it automatically when the program starts, or when you press the New button on the Game tab. The tournament will be "reset", setting the clock back to 0 and removing all buy-ins, etc. It resets the filename, too, so when you save your tournament, you'll have to specify a filename - no chance of accidentally saving over your template (unless you force it to do so).