So once the game is done how do i upload it to the site?

Its coming from unreal engine so im guessing i just click export and then upload or do i have to upload the whole zip file for the project?

You'll want to look into packaging your project here to get an executable you can upload to itch: https://docs.unrealengine.com/5.1/en-US/packaging-unreal-engine-projects/

You can find more information about uploading to itch specifically here: https://itch.io/developers