Integrating WordPress into my site

I’m very new to WordPress, but have it installed on my site and have been playing around with it a little. However, what I’m hoping to get some advice about is how to integrate this into my existing site. Right now, I have built a blog-like set of pages manually, and though that “news” appears on the home page for the site, there’s more to my site that is not blog-like.

What I’m hoping to do is replace the manually-created news with WordPress, but I want it to be transparent – it should look like my current site. I figured out how to embed the Loop in a test file, and that worked well… up until I clicked the title link on a post. So I think I need to develop a theme, but it sounds like themes require things like the CSS to be located in a single file in the theme folder, while my site has multiple CSS files stored in a folder at the root of the site. Since other pages not related to the blog use those files, I don’t want to bury them in a blog-specific folder hierarchy.

I’m sure someone else must have struggled with this, so I’m curious: is there an easy solution I’m overlooking? Or am I going to have to get my hands really dirty, bending WordPress to my needs in ways that will probably make it impossible to ever update it?

Thanks in advance!