What you want to do then, is to add all the files to CustomAssets. These will be enabled automatically when you start the game. Firaxis (as well as the modding community in general) does not recommend you alter the base game files.
For example, you are going to have to change the XML to add new civilizations. So, you create your own XML/Civilizations folder for your changed XML files, which you copy out of the base game files, and then change to your liking.
The Creation and Customization forum will have specifics on how to do this...and the tutorial above should have all the info you need.