So, is the IMU a separate board inside the Pixhawk? Is there information somewhere that shows which IMUs come with which FMUs?
The FMU is contains the control logic and the sensors while the IO takes care of the IO (duh) and some failsafe functionality which is best kept separate from the main loop.
Recent Pixhawk versions contain more advanced versions of the FMU board which hosts more than one IMU sets. To be more specific, they are populated with 2 or 3 separate accelerometers, gyroscopes and magnetometers. I'm not 100% clear if they use 3 9DOF chips or 9 3DOF chips to achieve this; it may vary from FMU version to FMU version.
That said, the FMU hosts one (or more FMUs) and not vice versa.