Building my website and then moving it to wordpress VS building a website on the

I have to build a website, and I need to know what is the right way to do it, since I don’t have a lot of experience working specifically with WordPress.
The only MVC I worked with was CodeIgniter and usually I code without any MVCs.
(I know that WordPress isn’t an MVC)
So I was asked to build a website for the company I work in – using WordPress.
Lynda.com’s theme building suggests first building the website and then copying the code to the relevant code parts to the WordPress files in the relevant parts.
The way I was asked to do it (since we don’t have a lot of time at work), is to write the code directly to the WordPress files, and learn to work with it through this process.

I’m not sure if it’s the right way to do it, and I’m almost sure that there is a clear yes/no answer for this question that I can get from experienced people.

My experience with WordPress is to change the 2014theme to a style that I want, adding my own php and jQuery code in some places.

If you know of good themeing tutorials I will be happy to hear how you started with ??

My website has to be less “blogish”. The request for using WP is for better user experience for my team.