Changing Images based on site area.

Hello WordPress,

My name is Lucas, and I’m absolutely new to using wordpress for websites. I have experience with programming both for computers, and for the back-ends of websites in the past, which is mostly limited to the .net platform, C++, Java, PHP, Mysql, CSS, and some old languages. So far making my first theme (as I teach myself), has been mostly painless and very interesting, however I have run into a bit of a snag, that I hoped someone can give me insight on.

Here’s the rundown, I have a site consisting of multiple pages divided into multiple sections, including a main splash page. The site itself is divided into the following format:
|—–Header—–| Consisting of mainly navigation buttons
|—–Secondary–| Consisting of a banner (changes based on section)
|—–Primary—-| The meat and Potatoes of the site
|—–Footer—–| Contact us, Etc…

Now this site starts on the Splash screen, which uses the standard header, a unique secondary, unique primary, and standard footer.

The other pages are divided into sections, each section (department) has a unique header to act as a banner, and each page has unique primaries.

Here are my questions:
1) what is considered best practice with wordpress? Using a conditional to choose which banner shows up in the secondary? Can you make multiple templates for a secondary section and choose them when posting a page? If so how?

2) On the main Splash page there are buttons in the Primary area of the page which when scrolled over change the secondary area to a different banner. This gives the illusion of a radial menu on the main page. This is easy to do in HTML and is actually live on the current page I’ve built, but will this be effected when the sections are split up? can I reference things found in the Secondary template from the Primary template? Does this require extra code? Or is it like PHP and since it is all printed on the same HTML page anyway you can write it as if they were a part of the same section?

I’m sorry if these are Noob questions, as I’m sure most of you know this all off the top of your head, but I’m still very new to trying to create a page in wordpress (without using a blog setup or a prebuilt theme). I actually have the entire website more or less built without wordpress, but I’m trying to teach myself to use wordpress as a content manager because I see a lot of potential in the plug in’s and the ease in which a non-developer can update a webpage which has a good theme. Any help or insight would be appreciated. Thanks!