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To give a new look to my website, I have added Javascript code which hides some elements and changes the order of elements according to my requirements.  the size of JS file is very small.

So , I want to know is it a standard way to get the job done?

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Yes that is one simple way to do it.

The preferred way would be to use a custom theme or plugin. So rather than having the elements on the page and hiding them with JS, they are not put there in the first place. It's a bit more complex but take a look at the theme docs for help.