Follow this step to edit the file in atom of file zilla

Edit -> Settings -> File editing

After this click on use custom editor radio button and locate your atom.exe or paste full path into that
And then click on OK to save the configuration.

To check whether it is working fine or not. just go to the directory structure right click on file select View/Edit it will open that file in atom editor.

/*
I hope it will help you.
Namaste _/\_
*/