This is where things are a bit messy at the moment. Where games support a controller, the ideal would be using as much of the controller mapping as possible to keep analogue movement and button prompts which match the controller, but replace the right stick with mouse control mapped to the touchpad. This is one of the default settings when you pick profiles ("Gamepad with high precision aiming" I think it's called).
At the moment, that doesn't work very well with a lot of games because they want you to use one or the other, and when you start aiming they freak out in different ways, like the framerate dropping to single digits in Lost Planet 3 when you start aiming.
So for those games you have to decide whether you make the right pad mimic an analogue stick, which works absolutely terribly, or you fully map the keyboard and mouse controls to the controller. The latter is by far the better option, but you lose buttons prompts matching the controller and being able to map analogue movement to the stick. That's not such a big deal in most things I've tried, you can make it so a modifier is applied when you push the stick all the way, so if there's a run toggle you can have that active when you fully tilt the stick. If there's a walk button, you can invert it so it's on until you fully tilt.
Hopefully developers will either start making native Steam controller mappings or at the very least allowing mouse input at the same time as controller input. Even without that, I'm finding that for anything involving aiming you can make a setup which works far better than dual analogues.