Hi,

Add js reference in the masterpage if your js file is needed in all the content page. If there is some js file specific to a content page, then place it in content page only.

While adding script block in the page(content page or master page), if your code is inside $(document).ready, then it does not matter where you are placing the code. Its upto your convinient. If your code is outeside of $(document).ready, then place the code block after the control to which the code is meant for.