Basically, there are two types of air flow controllers, the 'AFM' (Air Flow Meter), and the 'MAP' (Metered Air Pressure, I think..). The AFM uses a flow sensor on the end (or down the intake a little) of the throttle body, mechanically (but Electroniccaly controlled) allowing air to flow directly into the throttle body.
The MAP on the other hand is a vacum sensor that controls the opening of the butterfly to the Plunem chamber to allow air to flow to the cylinders this way. It is a slightly more precice way of mesuring air flow.
A Stand-alone ECU is just a box that controls particular components of the engine, by tricking the ECU into thinking it's doing all the work. A Stand-alone ECU can be hard to install, but once installed, it's essentially a set and forget thing.
um.... a stand alone system... you don't use the original ecu... the megasquirt IS the ecu.... you build it yourself, and then it's laptop programmable..... you can see how it's running and changes things whenever you want....