Generally speaking, the way to use git is to clone the entire repository. Based on the limited information you provided, I would recommend you have a separate git repository for this project. One repo per project or large portion of a project is fairly standard. It is not uncommon for a project to have a separate repo for the back-end server, the website, the game itself, and so on.
If the root of your question is about preventing git from storing/noticing changes in certain files, you can control that with a
Simple tool to get you started (enter