setting the work area has nothing to do with how the effect is applied. It is more for setting your render/preview length.
If you want to apply an effect to only a part of the layer there are a few things you can do:
1. Slit the layer (ctrl+shift+d) once or twice and only apply effect to the part you want
2. apply the effect, and then use keyframes within the effect to say when to have it on or off
3. put an adjustment layer only over the time to want to effect….then add your effect to the adjustment layer.
4. There are most likely more ways to do this, but these are just a couple that came to mind