You can configure the proxy for the Atom editor on Windows by modifying the file C:\Users\<your user>\.atom\.apmrc file.
- Add the below content to this file
https-proxy = http://server:port
http-proxy = http://server:port
- Exit Atom editor
- Open Atom editor again.
NOTE that you should not modify C:\Users\<your user>\.atom\.apm\.apmrc file as this file is auto-generated and any changes to this file will be lost upon re-opening the Atom.