Can I reply directly to confirmation emails or other messages I receive? If so, who receives my reply?

Yes, you can reply to most messages you receive from the company via Jobvite. Typically, the replies go to the recruiter working that particular position, but it is entirely dependent on how the company has set up their instance of Jobvite. So it may go to the hiring manager, it might go to a scheduler. I would reply, assuming it's going to the recruiter and the hiring manager, if that helps.