Use the context param this will say to waypoint where is your element scrolled (Search for $('#example-context') to see the context example)
$('#div-a').waypoint(function() {
console.log("waypoint a reached");
},{context:"#container"});
$('#div-b').waypoint(function() {
console.log("waypoint b reached");
},{context:"#container"});
I added an extra div to you page to test it and it's calling the messaged for each waypoint like this:
<div id="div-a"></div>
<div id="div-b"></div>
<div id="div-c"></div>