If you're talking about using Warp Stabilizer, just let it cook away, and start with a low number for your Smoothness setting--like, 5%. If that's not enough, then you can crank it up a little. Make sure to use the Detailed Analysis under Advanced settings.
If you're talking about resolving a couple of minor shakes, you can use the old-fashioned point-track stabilizers, and keyframe in and out of stabilized sections; i.e. when everything is fine, return the comp to its normal position and size.