This Zack doesn't use Atom, and never has.
I used to use Sublime Text 3 with a heavily modified version of Sebastian Lavoie's "Extendscript" package to easily execute scripts directly in AE. His version would copy scripts to specific folders and I found this unnecessary, so modified it to be more modular and execute scripts directly. You can find this here: https://github.com/seblavoie/sublime-extendscript
-- but I don't recommend this method anymore.
For general reference, "Extendscript" is the name of the programming language; "Extendscript Toolkit" is the IDE that Adobe supplies, but you really don't need to put any code in there in order to run it!
- Write your code anywhere you want, then in AE run the script directly via `File > Scripts > Run Script File...` and choose your script. Simple and easy. In recent versions of AE, there is a shortcut to run the last-executed script, so once you manually specify it once you can just hit the shortcut to re-run the new version.
- Use a script launcher like http://aescripts.com/kbar
with a button linked to the latest script file, so you can quickly just press the button to run the latest version of your script
- If you really want to use Extendscript Toolkit for some reason, just open the exact same script file in Extendscript Toolkit, and then every time you finish writing your code in Atom, and enable the ESTK preference to auto-reload the saved file. Then, every time you switch back to ESTK, it'll show the latest state of your script file. Then you can press 'run' in ESTK, and it'll be up-to-date with what you wrote in Atom.