Hi, this is me and my friends first game jam so we're a little unsure of how it works. Do we have to do the scripting in itch.io or can we use game engines like unity to make the game?

itch is just a marketplace and site for distribution - you can (and probably should, by default) use Unity or some other game engine :)

Any application file format-preferably, exe or an web game format like .js.  if possible, please compile it, thanks.