I use Yami's Overlay Mapping script: http://yamiworld.wordpress.com/yami-engine/image-display/overlay-mapping/ to accomplish what you are asking. You could have parallax a bridge you walk under and over by putting the bridge in the ground layer and a parallax layer, you could walk under it, and when you wanted to walk over the bridge you could change the parallax variable to use a different parallax without the bridge in it.
So just for example, X is whatever number you have your par variable set to in the script.
Variable X-1 has bridge and other stuff on it
Variable X-2 has no bridge, but the other stuff.
So to change from X-1 to X-2 when walking over the bridge, you'd control variable X = 2 in an event.