Add the FX to the clip, then use the Keyframing tool to set where you want to have the FX come in and go out. If you don't understand keyframing, there are some good tutorials on them on the http://www.vasst.com/login.htm site.
Another way of doing this is to split the clip (use "S" key) and apply the FX to only that small selected area. This is often the best way, as it's a faster rendering process in most instances.