Site structure question

Greetings WP.org. First post. yay.

I’m setting up my first wp site – and had a couple questions about site structure yall might be able to answer.

First off – I have a background of almost a decade of web development, including straight up html/css/javascript and a lot of flash development(as3). I’ve done very little work with php, but nothing I’ve looked at on the backend of WP is too confusing (okay, a little bit of the syntax is confusing, but I’m sure I’ll sort it out).

Anyway. My brand new site is going to feature just a few things: artsy code projects, a portfolio of illustrations and the like, and a blog section. The main index page is vertically organize into three main sections – illustrative / artistic code projects at the top, then a customized portfolio and then a chunk of excerpts from recent blog posts. The portfolio stuff links off to a main portfolio page, and blog links head off to the main blog section (into the interior of the wp folder structure).

My file structure looks like this: [css/img/js/php/swf/wp/xml].
I would very much like to keep my file structure separate from the interior of the WP, and rather, make calls up to the main directory for wp assets (rather than keeping assets in the internal theme folder). Make sense?

I know that I can add pages to the internal WP structure with WP tools, and create a static index wp page… but I’m unclear what gains I would receive working like that. At this point, I more comfortable working as indicated. (Though, I’d happily be educated, however, to the benefits of the latter.)

So, my uber-technical question: how should I go about manually pulling post excerpts onto this main index page (which is specifically not built via the standard ‘header,loop,footer’ logic sequence). What functions do I need to include, and in which order, to reach down into the wp structure, and return content (in this case, post excerpts)? I also will need to figure out how to customize excerpts.. but one thing at a time.

I’m developing via CS5 and an install of XAMPP.

Thanks in advance!!