Comments below this answer tell us that the Space Shuttle always remained in Earth's atmosphere. When it visited the Hubble Space Telescope or the ISS or Mir it was still in the thermosphere and simultaneously the ionosphere.
Of course the crew of any spacecraft in LEO will need to understand the impact of atmospheric drag since it has a continuous and significant effect on orbit altitude and phasing, and spacecraft attitude and tilt of solar panels can have a significant impact on that.
Question: But what (if anything) were crew taught about the ionosphere and its interaction with the Space Shuttle? Did they have to worry about spacecraft charging? Were there interactions between the ionosphere and communications systems they needed to understand? Were they briefed before launch on the effect of solar activity and space weather on the ionosphere and how that could impact aspects of a mission?