Hi bgurnee,
You have to upload two things:
First:
You program your game in assets. These can be music files, graphics and scripts. When you publish the game in a engine (for instance Unity) the engine will compile your game.
On Windows usually a YourGame.exe and a few folders. in order that we and the judges can play it you will need to upload this game to itch.io
and second:
The assets(.Mp3, .Png, .CS,....) with the source code . --> So mainly your Unity projectfolder...