1) The setup directions on their web page are actually pretty good, and it's pretty easy to set up.
2) Don't trust the salinity probe.
3) Don't trust the pH probes until after you calibrate. Get the 1 time use pH solutions (7 and 10 for a reef), use them, and then throw them out. They don't keep and they're only about $1 each anyways.
4) Once you get things set up, run it for a couple weeks and see what data comes in. Don't suddenly make drastic changes based on whatever you see.
5) Remember, instantaneous values are not long term averages.
6) Design your systems with backups. For example, my display tank temperature probe was a little too high and it sat out of the water when I shut off the main pump due to feed mode, or when the main pump ran dry due to the ATO running out of water when I was gone for several weeks without much planning. This resulted in the temperature prober reading the air temperature. Had it been a cool day this would have turned the heater on. Fortunately my heater also has an internal thermostat set just above my target temperature, but this would not have been the case with heaters that other people use.