I'm far from an expert on the subject since I've only brewed two batches on my new setup (direct fired RIMS), but I set my controller to the mash temperature and it seemed to work well. I'm measuring the temperature in a tee at the outlet valve on the mash tun. It stands to reason that if the temperature of the liquid coming out is at target temperature and you're recirculating, the mash should equalize at that temperature.