If you want to apply two different changes in both directions you need 4 waypoints; in this way you can 'define' the zone were the modification should take place. I've created a small Fiddle as an example, in this case the div become blue between 25% and 75% of the window height: http://jsfiddle.net/sandro_paganotti/mLAr2/
$("div").waypoint(function(){
$(this).addClass("blue").removeClass("red");
},{offset:'25%'});
$("div").waypoint(function(){
$(this).addClass("red").removeClass("blue");
},{offset:'24%'});
$("div").waypoint(function(){
$(this).addClass("blue").removeClass("red");
},{offset:'74%'});
$("div").waypoint(function(){
$(this).addClass("red").removeClass("blue");
},{offset:'75%'});