You cannot overwrite the scenario-setup, which is part of the game installation, by clicking on Save.
The Scenarios are generally installed in 'C:\Program Files (x86)\Civil War II\CW2\Scenarios', depending on whether you installed from Steam or choose to install the game.
All your Saves are in '..\My Documents\My Games\Civil War II\CW2\Saves'
When you start to play a Scenario, a new folder is created under the '..\My Documents\My Games\Civil War II\CW2\Saves' folder, generally with the default name of the Scenario, but you may change this name--which I generally recommend--go to Main Menu -> Load -> select the save of the scenario of which you wish to change the name -> click on the 'Saved Game manipulations' button in the upper right corner of the 'Load Game' window (with the computer chip icon) -> click on the 'Rename the game in selection' icon (looks kind of like a paper-folder) -> enter a memorable name for your game -> click the check-mark.
Now that Saved game(scenario) will appear in the Load Game window under that name.
When you have loaded your Saved game(scenario), the latest results of turn execution--the Saved_Game_Name.hst file found in '..\My Documents\My Games\Civil War II\CW2\Saves\Saved_Game_Name'--, and any orders you have saved since the last turn execution, are loaded.
When you click on the 'Save your turn' button in the upper right corner of the map--it should actually be called 'Save your orders', because that is what it actually does--, the orders you have issued since loading the Saved Game(scenario), which of course includes the orders loaded when you loaded the Saved Game(scenario), are written to the orders file of the loaded faction.
If you quit the game or re-load the Saved Game(scenario) without first clicking 'Save your turn', those orders you just issued, will be lost, whether you intended that or not.
In any case, you cannot overwrite the Game scenario through any actions you might take in the game interface.
If you wish to restart the a tutorial, simply go to the Main Menu, select New Game, and select the tutorial you wish to run.
Pay attention to the Saved Game(scenario) you load from the Load menu.