I know this does not answer your questions but…
If you are struggling with Atom try something else. I first tried Sublime and was not happy, so I tried VS Code and was much happier and have used it since.
To get started, if you haven’t already done so, you need to install git, and I would recommend watching a git tutorial on how to use the command line (it helped me anyway) to understand git better even though VS Code has a GUI for git, Atom might as well but I’m not familiar with Atom.