Inside Atom, navigate to Preferences (or Settings) → Install and search for wakatime.
Click the Install button.
Click the Settings button inside the wakatime package.
Enter your API key
Use Atom like you normally do and your coding activity will be displayed on your WakaTime Dashboard.
Note: The leet way to install WakaTime is with this Terminal command:
apm install wakatime
The plugin will be kept up-to-date automatically.
Inside Atom select Preferences… or Settings (depends on the system) → Packages and search for wakatime.
Click the Uninstall button.
Also make sure to delete your api key from ~/.wakatime.cfg to keep your account secure.