First, make sure you have the recent 'San Francisco' release and the right Shuttle (there's a legacy FDM for the final glide phase called 'shuttle' and the new orbiter called 'SpaceShuttle'). Make sure you start with a mission phase tag --aircraft=SpaceShuttle-launch for instance) otherwise it won't be in the right config.
Then, the Shuttle is a complex machine. You can actually use the original NASA manual (it comes with the Documentation/ folder) to understand how the systems tie together, the majority of the systems works just as described there.
A level lower, there's extensive wiki documentation on the
Space Shuttle page and the linked pages for the various mission phases and the avionics, including some on-orbit tutorials teaching you how to go from MECO to an insertion burn and how to operate the data processing system, manage the payload bay doors, the coolant loop systems and the Ku-antenna.
It depends on what you'd like to do. Pick a single mission phase (say the final approach), read up on the theory of what you should be doing, learn to fly it (I picked final approach because it's just flying by what you see, there's little avionics you need to learn). Then go a step back, read up on a TAEM pattern and learn to fly the TAEM phase and how it merges into final approach.