I don't understand why the msfs 2020 is partly on 1 drive while the main program is on another?

I installed the sim to my Games directory during the first install. This created a basic file structure that has no actual game files in it but instead stores all of the add-ons for MS and 3rd parties Eg. C:\Games\MSFS\Community or (Your installed drive & folder)\MSFS\Official\OneStore.
All of your terrain/airport add-ons purchased ‘with’ the game will be here. 3rd party(Orbx etc) add-ons will have ‘Links’ to those 3rd party install folders in the Community directory.