Hi Durovnax!
We have a great support page concerning the use of the Animus Control Panel, check it here.
To answer you:
Applying ACP settings to a save file (hacking the Animus) will create a copy of the save file you selected. This allows you to resume your game unaffected by ACP settings later, if you wish. You'll be able to distinguish the ACP save game from the normal save game by the note Animus Hacked underneath the save file name.
Tell us if that helps!![]()