HTML/CSS site to WordPress

Greetings!

Alright, so this is my first attempt to create a WordPress theme from scratch,
because my client needs to have the option to upload/change dynamic content to
their site, and they have deliver the exact layout for it.

So, for this project I did a Photoshop mockup of the design, and then created
a full HTML/CSS site , thats its ready and you can see a demo online on this URL:

acdemo.filete.net

If you check the site, all the grey squares you see, and the PORTFOLIO page
needs to be manage thru the Worpress back-end.

Well, the way I see it, the site its pretty simple, but I am still learning the structure
needed for this task.
I was able to break the HTML and create the basic theme in terms of design with the files (index.php, header.php, sidebar.php, footer.php and style.css).

I also understand that is the _loop that creates the CMS for the wordpress, so just for testing, I have copy the PHP code for the PAGE loop inside the main content <div> in the Home page of the site, and indeed by creating a new Page in wordpress and named HOME I was able to upload a picture that have show inside the <div>.

I have so many questions, that I will probably break into different forum posts
and hope to have the help of the great community here ! 🙂

There so many things I dont get it but I really need/want to learn,
so on this post I just start with these issues:

1. How can you make the HTML/CSS menu functional and add the other HTML pages?
2. And if your design uses several CSS files, where and how do you link them?
3. if the HTML div´s have specific size, why does the content uploaded using the WordPress backend (a picture or video ), if its bigger in size its just goes over the div?
How do you fix this issue?

Like I said, as I am trying to develop this project I will keep asking for help,
but I dont want to create long posts, just like this one already is ! 🙂

Thanks for all the help!