Are we required to upload our files to GitHub and would it just be the project folder? What if I want to place secrets in it (< most important)?!
Yeah, but if you have secrets (assuming you're talking about passwords / other credentials) you can leave them blank in the code/config files and maybe just leave a note in the README file. Ideally, people will be able to take entries and build them themselves.
It's probably overkill for a game jam, but GitHub has concept of secrets that you can tie to a repository depending on how you decide to build/deploy your game. My guess is that you can skip it for this though.