Once in orbit, You activate OPS-201/VC Control or OPS-202/VC control. This creates a totaly different VC from the one with shuttle fleet (called STS VC) . You now are looking at the aft workstations. This is when the controls listed in the payloads manual are active.
M = middeck view
This is where you will notice a difference is you are using SF 4.0.0. Payloads was for the previous version when the MFD were painted as textuers. So when you switch to the STS VC the MFDs are no longer functional, which isn't a problem. Other than this everything else works fine. To have the reentry effects, follow the precedure for reentry in the Payloads manual.
zerofay32
edit: You only have, or need, the STS VC and Middeck view while your in orbit.