Code structure and necessary elements in web development

I'm thinking of developing a database-based web application from scratch but I have some concerns. I'm quite new to the world of web development (I've done Harvard's course CS50, but that's about as far as my knowledge goes) and I've recently tried wordpress a bit.

Something that confuses me is how many different files, how extremely much css and how many different nested divs there are in most wordpress themes, but also on any website in general. This makes me anxious, since I feel like I will miss so many things by starting from scratch.

My questions are basically:

1. Are all the css rules, nested html divs and php-code necessary or are they to some extent a product of copy-paste (in the case of wordpress themes specifically). If they are necessary, what does it all do? Could someone give me a brief overview of the thousands of lines of css and tens of php-files?
2. What are the best practices when building a website from scratch? How should the structure of the html look like (especially considering nested divs), how should I build up the css file and what code is important to include? I guess I'm looking for an explanation of the structure of development and a description of a template of code (html, css and php) that you should always include.

I'm planning on building a serious, secure and well-functional web-application and that's why I want to follow the best practices and understand the purpose of all the code. Thank you in advance!