The area will be moving, wiggling about and such. I tried a mask, but after I set the mask where I wanted it to be, I couldn't figure out how to show the whole comp again... (See image)

EDIT: Figured out how to show it, now how do I make it so that the mask controls the effect coverage? Cause right now the mask is doing nothing.

EDIT: Figured it all out:

First duplicate the layer you are going to be applying the effect to (Control+D).

Next set up a mask on the layer on topmost layer, make sure that the box beside the word "Mask" is set to "Add".

Then set up your effect.

I think that's it... See screenshot.