Could you please start by following the Brainstorm introduction tutorials, using the example dataset provided, and then go through the OpenMEEG BEM tutorial using the protocol "TutorialIntroduction"?
https://neuroimage.usc.edu/brainstorm/Tutorials
https://neuroimage.usc.edu/brainstorm/Tutorials/TutBem
This would probably point out what you are doing incorrectly.
If you ended up with messed up anatomy folders, there are probably things you are not doing right, and it will be difficult to debug if we are not starting from a solid ground.