is there a way to visualize the command history so I can do it manually and copy it to my script?
Unfortunately, not yet.
This is part of our roadmap for the developments of the next two years.
The Scripting tutorial include lots of information about writing scripts with Brainstorm:
https://neuroimage.usc.edu/brainstorm/Tutorials/Scripting
You can try searching for functions from the callbacks of the GUI elements:
https://neuroimage.usc.edu/brainstorm/Tutorials/Scripting#Find_interface_callback_functions
The menus for loading atlases in the Scout tab are all defined in function panel_scout / CreatePanel.
If you can't find what you are looking for, please describe exactly what you are trying to do, including screen captures.