Once you have changed the graphics and saved it, you then go to
FILE>Make Install Script and that will make a .aks which you then just click on and it will start the game for you.if you want to restore it, open up the project that you changed the samurai into a ninja, click on the Resource (essentially Unit) that you created then click on RESTORE and then save and once again go to FILE>Make Install Script and give it a different name and click on it to start the game and install it
Specs: AMD Athlon X2 4600+
2GB RAM
ATI Radeon X1900XT 512MB
300GB HDD