So, I've been working on trying to integrate my website and blog (I'm not using a theme because most of the site's content is going to be non-WordPress dynamic php stuff). It's just starting to work. The WordPress header is included at the top of my index page and whenever a visitor is in my site's home section a php file containing the loop (nearly identical to the default theme's index) and post formatting is called up between my own header and footer. This is all well and good, but I'm not getting all my posts, nor do my post's links seem to do anything but reload the same content.
Thus, I'm wondering whether I can get all the functionality of a theme by using my WordPress blog as an include. If I understand everything the Codex has said about Themes and the loop, specifically I'm wondering if it will be possible for me to use templates (Just as though I was using a theme) but to store them in a non-Wordpress directory. Could something like this work?