You can configure the proxy for the Atom editor on Windows by modifying the file C:\Users\<your user>\.atom\.apmrc file.

  1. Add the below content to this file 
    https-proxy = http://server:port
    http-proxy = http://server:port
  2. Exit Atom editor
  3. 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.