I am deploying my documents automatically to the server.
When I save my .less / .sass files, the File Watcher transpiles them, but only uploads the source files, not the transpiled .css file.
Is there a way that the .css file is also being deployed?
Make sure to tick the 'Upload external changes' checkbox in Deployment/Options. This option makes PHPStorm upload the files changed by a third-party tool (LESS compiler in your case). See http://www.jetbrains.com/webstorm/webhelp/deployment.html and related topics for more info