I use my HERMS on the TopTier -- HLT w/HEX at the top, MLT middle, and BK on the bottom. I use two pumps: pump 1 recircs HLT water to keep a consistent temp in the HLT. Pump 2 is used during the mash -- I recirc for 90 mins from the bottom of the MLT up to the HLT, through the HEX, and then back into the top of the MLT.
I also use two Ranco probes to automate things: one probe monitors the HLT temp. The other monitors the mash. The HLT probe is what I use to maintain the temp. Usually, there's a 1 or 2 degree differential between the HLT and the MLT-in -- so I set my HLT temp to, say, 154 when I want to mash at 152. Rock solid.
I'd hoped to move the probe to the MLT-in (since all I care about is the temp of the mash going into the MLT), but I haven't gotten around to it. Once I move that, though, I'll not worry about the HLT/MLT differential. I'll just set the MLT-in temp to the mash temp, and let the HLT adjust accordingly. I use the other probe in the mash as a double-check to make sure my main probe is reporting the right temperature. I've also got an analog thermometer on the MLT-in that I can see from a distance and make sure everything is okay going into the MLT.
I mash thin and always use rice hulls, so the mash temp is pretty consistent throughout (and gets up to temp very quickly after dough-in). Since I started mashing thin (1.9 to 2qts/lb) and using the rice hulls, I've never had any recirc problems or stuck mashes (even with big rye and wheat beers). I usually make sure my HLT water is 14 degrees or so over my mash temp at dough-in. Then I add the grains, stir, readjust the HLT temp back down to a degree or two over my mash temp (and have to add a bit of cold filtered water to the HLT to drop the temp). Within 5 mins, the grains are exactly at my mash temp. Then I take the pH readings and start watching pH for the next 15 mins or so to make sure I'm within the 5.3 to 5.5 range. If I'm too high, I'll add either lactic or phosphoric acid or occasionally grind an ounce or two of acid malt and stir it back in the mash. I acidify my sparge to pH 5.8 or so with 1.5 to 2 teaspoons of 85% phosphoric acid (I have pH 7.7 water). Whatever HLT water is left over after the sparge, I'll use for cleaning after the brewing is finished. I also use a charcoal filter for all water and then a single campden tablet in the HLT when I first fill it.
I fly-sparge for 45-60 mins and move the wort via gravity from the MLT to the BK. The wort is absolutely crystal clear going into the BK (even though I won't see it that way again for a couple months until it clears in the bottle).
I use 3 Blichmann 15 gallon kettles, 2 March pumps, copper coil for the HEX, about 20-30 feet of 1/2" silicon tubing, and 5500W elements in the HLT and BK. I use HighGravityBrewing's control panel with a 220 outlet. (I had the outlet professionally installed and weather-proofed with all the safety stuff -- so that was a bit of an expense.)
I can't imagine going back to propane after this electric HERMS. It's still a long brewday (mostly due to the 90 minute mash, 45-60 min sparge, 90 minute boil, and cleaning I do) but it's worth it. If I start brewing on a Saturday morning at 7:30a, then I'm usually putting away the last of the gear and heading back inside by 3p. Love the system. I usually get anywhere from 75% to 85% efficiency.