I have to make sure we're talking about the pure distinction between mechanical, direct-drive superchargers, and exhaust-driven turbo-superchargers.
That said, either method will work quite well in FSX/P3D.
You mention two-stage, but what you really mean is two speed, that is, high/low blower speeds. The stages of a supercharger are something altogether different. FSX doesn't care about the number of stages, it just reproduces the horsepower of the entire blower at a given RPM/altitude/boost, as a single unit.
The gauges discussed are sort of a boost-cut out simulation. In real planes, such as the Spitfire, which used these devices, boost cutout is just a physical block of the throttle to keep the pilot from overboosting the engine on takeoff. It's a crude device and is not connected to the engine directly. At higher altitudes it can be moved out of the way to allow for full throttle opening. But this isn't what you're wanting, I don't think.
Two-SPEED superchargers are not modeled in FSX/P3D, but some folks have found very clever ways to make it appear that they are.
Personally I use only the native FDE for everything and have done for over 20 years. It's cleaner that way.
For a real crankshaft-driven super charger, the boost factor will need to be adjusted to provide the appropriate powers at specified altitudes, and that figure is usually somewhere between 2.5 and 5 but of course will vary depending on the engine. There are sometimes two boost factors in the .cfg file but we only need the high level boost, the low level factor does nothing.
A supercharger gains horsepower with altitude due to the air being thinner, which reduces exhaust back pressure. So you usually have a much higher bhp value at some altitude than at sea level.
The annoying thing about superchargers is you will have to manually adjust the throttle at all times and under all conditions since an automatic boost control is not incorporated in the native FDE. But they work well if set up correctly.
Turbochargers have automatic boost control, and one can emulate a supercharger equipped with automatic boost control pretty well by simply using turbosupercharging.
With turbos, one needs to set the critical altitude somewhat differently than that specified for the supercharged engine one is modeling, as FSX calculates BHP gain with altitude quite differently for each method.
The supercharger entries in the .cfg file can be deleted completely if turbocharging, but the turbocharged=0 flag must remain if supercharging. They don't work together in any way, so a critical altitude value for a supercharged engine does nothing.
