I have a similar setup - single tier, three pumps, some hard plumbing and valves so I don't have to move any hoses. I have 15 gallons pots and a false bottom in the mash tun. I started doing protein rests and it improved my efficiency dramatically. I do a 122* protein rest and when it's time to go to the next step, I turn on the gas and the pump to recirculate - always have the pump on when the gas is on to avoid scalding and just plain too much temperature differential. It is unique to each setup but I think one of the most important things is knowing when to turn off the gas to avoid over heating the mash. If I want to heat from 122 to 151, I turn on the gas and pump and then watch it like a hawk until the temp goes to about 149, I then turn off the gas and leave the pump on until the temperature gets to 151 and stays there for a few minutes.
The one thing to watch out for with this setup (at least for me) is to not get distracted when the gas is on the mlt. I always try to make sure I sit down in front of the mlt and watch the temperature very closely to avoid over heating.
After a while, you can develop a routine and have some sense of how things are going to behave. I dough in when the water is about 100* and heat to 122 for 10 minutes, then heat to my sacc rest temp for however long (usually 45 - 60 minutes, occasionally 90), then heat to mash out (168*). I like to stir the mash at dough in very thoroughly, then again when I am going from 122 to the sac rest, then again 30 minutes into the sac rest and at the end of the sacc rest. Depending on the mash and the outside temperature, I may turn the gas on for a minute or two when I'm stirring at 30 min into the sacc rest to keep the temperature up. If I don't I usually only lose a degree or two but one minute of gas can maintain the temperature pretty close to target.
I also don't continuously recirculate - I turn on the pump when the gas is on and when waiting for a temperature to stabilize, and for about 10 minutes prior to first runnings. Some like to have the pump on 100% of the time, but I don't see the need for it if the mash is well mixed.
I batch sparge, so I can't tell you too much about fly sparging. Lately, I've been getting mash efficiency in the mid to high 80s which is a big change from a while back.
Another habit I picked up is to not heat up the mlt until I start the heat to mash out. This may be different since you are fly sparging but having extra water at room temperature allows me to cool down the mash quickly if I over heat it. If I see the temperature climbing fast, I set the valves and turn on the hlt pump for a minute and it usually stops it.
I also suggest calibrating your thermometers before your first batch - temperatures are critical and you may find thermometers off by 4 - 6 degrees which could be a problem if you don't know it ahead of time. There are several methods for calibrating thermometers and usually an adjustment nut on the back of dial thermometers to do it.
Anyways - I like my current setup. It's simple to use and I get great efficiency. I have tried several automation setups (want to buy one?) and ended up spending more time dealing automation problems than making beer so I finally just pulled it all out. I find that having a simple manual system works fine and really only takes a little more attention.
