you don't need separate document.ready
blocks all could be done in one wrapping block
$(document).ready(function(){
$(".ease").slideUp(1).delay(400).slideDown(700);
$('.menu>li').hover(function(){
$('.menu>li>ul').stop(true,true).slideDown(400);
},
function(){
$('.menu>li>ul').stop(true,true).slideUp();
});
});
In order to structure the file properly I'd say have one file which is for the core functionality and more precisely you should have separate files for templates, components and modules. for example:
Template
templates/my_template/js/scripts.js
Components
components/com_test1/js/script.js
components/com_test2/js/script.js
components/com_test2/js/script.js
Modules
modules/mod_test1/js/script.js
modules/mod_test1/js/script.js
modules/mod_test1/js/script.js
This way things will be clear what file is responsible for what piece of code. In the files itself if they become quite big you can add some annotations for example:
(function($) {
# 1. Main menu
# 2. Accordion block home page
# 3. Lightbox/Pop-up overlays
# 4. Tabbed content
# 5. Misc
# 1. Main menu
$('.main-menu').on('click' someFunction);
# 2. Accordion block home page
$('.accordion').on('click' someFunction);
# 3. Lightbox/Pop-up overlays
//...
})(jQuery);