All what air? Regardless of how much that supercharger is turning think about the throttle body. It regulates how much air makes it to the SC. At cruise or low throttle the throttle body is barely open thus not much air is making it into the supercharger. The output of the supercharger is very little because it isn't moving a lot of air...less than the vacuum created by the engine naturally. Because of this, there is a negative pressure (vacuum) in the Lower Intake Manifold and this keeps the Boost Bypass Valve open letting that little bit of air bypass the supercharger completely.
When you mash the gas, more air is coming through the Throttle Body than the engine can pull in on its own and the blower will now be able to build boost in the LIM with that extra air. When there is positive PSI in the LIM (Boost) the Boost Bypass Valve closes and 100% of the air going through the TB is getting into the SC.
Does that help? I think I explained that alright.