How to change the menu position using the scrollTo function?

I am making a website and created a menu with anchor that has the effect of scroll with Javascript. So that's fine, the only problem is that I need to when Javascript takes action the content always stays under the menu, but I did not find where to set it.

This is the code that goes directly on the page:

<script>
    $(document).ready(function(){

        /** 
         * This part does the "fixed navigation after scroll" functionality
         * We use the jQuery function scroll() to recalculate our variables as the 
         * page is scrolled/
         */
        $(window).scroll(function(){
            var window_top = $(window).scrollTop() + 12; // the "12" should equal the margin-top value for nav.stick
            var div_top = $('#nav-anchor').offset().top;
                if (window_top > div_top) {
                    $('header').addClass('stick');
                } else {
                    $('header').removeClass('stick');
                }
        });


        /**
         * This part causes smooth scrolling using scrollto.js
         * We target all a tags inside the nav, and apply the scrollto.js to it.
         */
        $("header a").click(function(evn){
            evn.preventDefault();
            $('html,body').scrollTo(this.hash, this.hash); 
        });



        /**
         * This part handles the highlighting functionality.
         * We use the scroll functionality again, some array creation and 
         * manipulation, class adding and class removing, and conditional testing
         */
        var aChildren = $("header li").children(); // find the a children of the list items
        var aArray = []; // create the empty aArray
        for (var i=0; i < aChildren.length; i++) {    
            var aChild = aChildren[i];
            var ahref = $(aChild).attr('href');
            aArray.push(ahref);
        } // this for loop fills the aArray with attribute href values

        $(window).scroll(function(){
            var windowPos = $(window).scrollTop(); // get the offset of the window from the top of page
            var windowHeight = $(window).height(); // get the height of the window
            var docHeight = $(document).height();

            for (var i=0; i < aArray.length; i++) {
                var theID = aArray[i];
                var divPos = $(theID).offset().top; // get the offset of the div from the top of page
                var divHeight = $(theID).height(); // get the height of the div in question
                if (windowPos >= divPos && windowPos < (divPos + divHeight)) {
                    $("a[href='" + theID + "']").addClass("header-active");
                } else {
                    $("a[href='" + theID + "']").removeClass("header-active");
                }
            }

            if(windowPos + windowHeight == docHeight) {
                if (!$("header li:last-child a").hasClass("header-active")) {
                    var navActiveCurrent = $(".header-active").attr("href");
                    $("a[href='" + navActiveCurrent + "']").removeClass("header-active");
                    $("header li:last-child a").addClass("header-active");
                }
            }
        });
    });

</script>

And this is the Javascript code:

$.scrollTo = $.fn.scrollTo = function(x, y, options){
if (!(this instanceof $)) return $.fn.scrollTo.apply($('html, body'), arguments);

options = $.extend({}, {
    gap: {
        x: 0,
        y: 0
    },
    animation: {
        easing: 'swing',
        duration: 600,
        complete: $.noop,
        step: $.noop
    }
}, options);

return this.each(function(){
    var elem = $(this);
    elem.stop().animate({
        scrollLeft: !isNaN(Number(x)) ? x : $(y).offset().left + options.gap.x,
        scrollTop: !isNaN(Number(y)) ? y : $(y).offset().top + options.gap.y
    }, options.animation);
});
};

Here is the link for the site I'm doing . #.