Yes, I think you should really resign because from what you wrote, you are saying the guy is the only person in the company that know how to use the system? And he can do 60% of your job including conducting meeting, all without your supervision?

Sound like he should be the manager of the company, managing everyone, including you instead of you supervising him.

You can't do anything beside just open a topic on public forum to rant? Better quit as soon as possible, to not jeorpardize your CV.