It seems that you’re having each section on a different page/URL and not on a single page. That’s why the plugin doesn’t do anything.
The thing is, even if you added an extra script in your document to make the plugin animate each separate page to its section, it wouldn’t make any difference. Your sections are at the top of each page, so the plugin wouldn’t have to scroll anywhere (as it’s already there).
I’d suggest creating a single-page website, meaning putting all or most of your sections on one page. Using the plugin in such layout would make more sense.
If you still want to use a different URL for each section and have the plugin animate the page on page load, you can use the following script which you’ll have to add it in your theme (e.g. in footer.php) manually:
<script>
(function($){
if(location.hash){
$(window).scrollTop(0); //stop jump to hash straight away
setTimeout(function(){
//stop jump to hash again a bit later
//for browser compatibility
$(window).scrollTop(0);
},1);
}
$(window).load(function(){
if(location.hash){
setTimeout(function(){
//use page scroll to id scrollTo method
//to animate page to location hash
$.mPageScroll2id("scrollTo",location.hash);
},1);
}
});
})(jQuery);
</script>