I had the same initial problem with my steam controller reported in many sites, even in the Steam forums, so, for the record, after a headache trying many things, finally I made it this way:
- First, I tried to connect using the bluetooth interface. At this time, I could use the Steam Controller (SC now on) partially, and wasn't cool....I could not even play a game.
- Next, I figured out that in the Big Picture Mode there's an option to add the control, and in fact, it tried, but it didn't work. A window asked me to press Steam button + X button at the same time, but it didn't work neither.
- Next, I read that turning off and on the computer might help, and yes it worked a little bit. Restarting the system made that Steam asked for the controller the next time I opened it. But, still didn't work properly, so that, I read on Steam FAQ that connecting a miniUSB wire could help. And yes, definitely it's started to work.
- After connecting the wire, the "Add SC" started to work, but there was one last step left.
- In order to make it work better, the SC has something called "templates", that it's nothing else than a preconfigured settings depending on the game, or kind of game, shooter, platform, etc.
- So, I selected the best I could see and that's all.
Hope it helps who's still a lost soul like I was once.