Did it not come with a manual? If it didn't you can open one from their website
http://www.neptunesys.com/images/dow...3_3.20_web.pdf
I was confused as hell when I first begun using it too... Eventually you get the hang of it though and then its pretty easy.
Re-set the controller to its defalt settings so that you're starting fresh (its explained in the manual) and then re-calibrate your pH and ORP probes but leave the temperature probe alone unless it seems really inaccurate. That is what I would do. I actually went so far as to test the temperature probe of my ACIII against a lab grade thermometer at our university and it was dead on.