I haven't been able to figure this out yet. Atom seems to use spaces as the default indentation mode. I prefer to have tabs instead though. Sublime Text has built in functionality for switching and converting indentation.
Anyone found out how to change the indentation mode of Atom?
Some screenshots from Sublime Text:
See Soft Tabs and Tab Length under Settings > Editor Settings.
To toggle indentation modes quickly you can use Ctrl-Shift-P and search for Editor: Toggle Soft Tabs.