Just set in and out points for your clip. Warp Stabilizer will only work on that part of the clip.
Sorry for the noob question, I'm brand new to ae. This is how far I got, I imported a clip into ae. Created a composition. I can set the in and out point in the footage tab, but I can only drag the warp stabilizer onto the footage under the composition tab, which in turn stabilizes the entire clip not just the region between the in and out points.