With a controller plugged in click on the controller config button on the game's library page and something that looks like this should pop up: (If the screenshots look different then that is cuz i am on the Steam beta)
Now click on the big button under current layout and something that looks like this should pop up:
Now click on the community layouts button and click on the layout that says OTHER LAYOUTS ARE OUTDATED in it's bio BTW if none appear for you then click on the show all layouts button at the bottom.

Now that your in-game the controller should work just fine. Just make sure your using the mouse in the menus.