Where should I upload the JS CSS and images files to the server

It doesn't matter where you upload your js, css, html and images. It matters whether your links or file paths in your page(eg. HTML file) and CSS code are correct.

There are two ways to specify the paths. One is absolute, such as "/level1/level2/level3/myjs.js"

The other is relative, such as "level3/myjs.js"(assuming your page is located in level2).

If you are using relative path, you need to pay attention to the images specified in your CSS file. The relative image path in your CSS file should be relative to your CSS file location instead of your page location.  

Thanks for your guidance.  

I appreciate this guideline. Thanks