You can use bypass valves to bypass the supercharger (roots) as once the turbo is making decent boost the supercharger isn't needed and is probably causing excessive heat for little gain. The problem with this is getting the changeover from one to the other right.

You don't have to use a bypass valve for that purpose but your air temps will be higher so you need better cooling. On the plus side you don't have the complications of of sorting out the changeover bit out.

You DO use a bypass valve for stopping the supercharger producing boost at idle and blowing your inlet apart

There is some debate as to whether the S4 only used the bypass for idle or not as I'm sure Stavros will point out.