All of the Settings (Ctrl+,) are stored in the ~/.atom directory, specifically:
atom -h
Atom Editor v1.7.2
Usage: atom [options] [path ...]
One or more paths to files or folders may be specified. If there is an
existing Atom window that contains all of the given folders, the paths
will be opened in that window. Otherwise, they will be opened in a new
window.
apm help install
You can add more than one directory to your current Atom window, by choosing “File » Add Project Folder…” from the menu bar or hitting
# open both the hopes and the dreams directories at the same time.
atom ./hopes ./dreams