My Megasquirt adventures over the years
I didn't touch too many of the other settings in this tab. I believe several are only used based on which control algorithm you pick.

Engine state settings is useful to set up, but as best I can tell doesn't really do too much right now. These values define general conditions your engine is in that can be used for some other settings. The primary uses are the VSS threshold (for idle control), the TPS closed, and the overrun for stuff like cutting fuel while coasting. Otherwise, they are just handy for datalogging to see what your engine was doing at a glance.
The fan control page has some novel settings, but is pretty dependent on what fan setup you have to begin with. I could theoretically run a mechanical fan on my truck water pump, but I have some generic dual electric fans on the car right now. I got a little clever with my wiring and opted to run them independently as I wanted one fan to run all the time when the A/C was on, but the other to only come on as needed when the temperatures went up. I have mine set up to bump my idle slightly as well because they hit the electrical system pretty hard when they come on. I also recently adjusted them to turn off over 40 mph because my A/C could keep up fine at that point. Lots of fun little stuff you can do on that page like having them shut off at WOT as well if you wanted that little extra bit of power.
Alternator control was another big update I did on my car with the MS3X upgrade. I was originally running an old factory voltage regulator, but it looked like I was melting the silicone potting compound out of it and I'm not sure it was built to handle the field current of my modern alternator. I got to looking and found that the MS could control it for me, and I had a spare high power output available, so I made the swap. The main control settings were found via the Megasquirt manual. The other values you can play with as they suit you. I have mine set up to drive the alternator a little harder after startup to top the battery off from the starting event, then taper down to a lower voltage for normal running. If you add battery temp or current sensors you can get even fancier, but my car is still pretty basic as far as electronics are concerned, so I kept it fairly simple. So far it seems to work great and it got one more thing off my fender.