Schematically, this is how the game refers to the mannequin files and how they refer to each other:
It is simplified a bit as ADB files, FragmentID Definition and Tag Definitions can hierarchically refer to other files of their own type. And FragmentID definitions can refer to Tag Definitions to define FragmentID-specific Tag Definitions.
The editor runs independent of the game, so has to use its own setup file. Compare this picture with the picture above, the setup file effectively replaces whatever setup the Game Entity uses. The Sequence file is independent of all this.