I would like to know the proper way to add new javascript files to RT and also where should I add the <script src="newJS.js"></script> tag.
You can follow the rules for CSS provided in the custom styling documentation but replace 'css' with 'js' and use the @JSFiles configuration option rather than the @CSSFiles option. Once you do this, RT will then pull in your JavaScript for you, so you don't need to add the <script> tags yourself. You can also put <script> tags right in the style box in the Theme Editor.
If you want to put JavaScript at specific parts of the page, you can use RT's callback system, described in the extensions documentation. But for smaller customizations, you should be able to manipulate the DOM from your main JavaScript file.