Supporting controllers on PCs still is a pain for some reason.  Here's our method for solving the problem:
• Open Steam, go into Big Picture Mode, open Settings, and configure your controller bindings.
• Go to ~/.local/share/Steam/config/ and open config.vdf with a text editor. (Notepad will suffice fine)  
• Find a section that looks like the following:
"SDL_GamepadBind" "38076382000000000000504944564944,MLG Gamepad PS3,a:b1,b:b2,y:b3,start:b9,guide:b12,back:b8,leftstick:b10,rightstick:b11,leftshoulder:b4,rightshoulder:b5,dpup:h0.1,dpleft:h0.8,dpdown:h0.4,dpright:h0.2,leftx:a0,lefty:a1,rightx:a2,righty:a3,lefttrigger:b6,righttrigger:b7,x:b0,"
• Paste the giant string into the response below
• The next update of the game will include your controller!