New design

Hello Boys,

I have a webpage (html, css, js), nothing fancy. It has 3 pages (index, about and collection).
I am in need of pushing this design to nopCommerce, the problem here is, I need the page collection to have the functionality of eshop. I don't mind having this functionality all over the webpage, but I would like to hide it where it is not needed. I went through some posts here in the forums, but I don't think they answered my questions.
Long story short, I need to delete design of nopCommerce and put there my own and implement nopCommerce functionality over it. So, my thoughts are -
1) Do I need to alter MVC in some way to cut parts of nopCommerce I don't need and add my stuff or would it mess up references and later on, if I add stuff, would it mess with administration panel?
2) Would it solve this for me, if I just modify master pages or/and page content in 'views'?
3) Any other possibility? The less time consuming and confusing, the better.

Every opinion is appreciated,
Thank you in advance!!!

Please check the corresponding documentation

I fear this might not solve my problem. I have already went through docu.. And what you linked is just modifying design. What I need is to modify design and replace or completely remove some of the elements. That is why I believe I have to modify views in MVC as well. Or am I wrong?