I’ll be posting some extensive theming documentation next week which might help point you in the right direction (although given the content of the post its unlikely to cover every point of contention you have.) It’s more geared toward starting a theme from scratch rather than forking Atomik, but maybe it will help.
Regarding the original post, I see more general frustration than specific questions. The only specific question I see that I can suss out is number 4.
- If you’re trying to just add custom styles directly to the theme (if you’re building your own version of Atomik) then you can put them anywhere, and recompile the theme.
- If you’re trying to use the built-in customizer (which it seems like you might be doing), then the custom CSS selector can be found here, at the bottom of the customizer, where the title says “Custom CSS”, and the button has the label “Add Custom CSS”.
Turning this on gives you a button to pop open a custom CSS dialog, just like in version 8.
Changing this and saving as a new skin will apply your custom styles.