Set up the tournament the way you like it. Save it as a new file named something like "my-tournament-template". Go to the Preferences tab and press the Config Files button. The very first entry is Default Tournament. Press the Browse... button and find your tournament file "my-tournament-template". Press the OK button.
Now every time you launch the application, the TD will load this tournament, reset it to a pre-start state (no buy-ins, tournament hasn't begun, but players, if you have any added to it, will still be there), and clear the filename (so you don't accidentally save over the template).
Any time you want to start a new tournament, press the New button on the Game tab and select the option "Create a new tournament using the saved tournament 'my-tournament-template.tdt' as a template...". Same results.