Question:
I want to keep my regular subpages on my site (example: mysite.php portfolio.php,) but I want to use wordpress as well for the theme and use my own subpages instead of the wordpress pages. How do I use my wordpress theme on my regular subpages?
Check out the answer(s) below…

There are a few ways to do this.
1) You can create post or page redirects in WordPress to point to your static pages. Here’s an article I wrote about it. http://bestbloghost.net/how-to-create-a-wordpress-postpage-redirect/
2) The new 3.x version of WordPress now comes with menus. Go into your Dashboard > Appearance > Menus to create menus that can then be used as widgets. In there you can select pages, posts, categories, etc. to appear in a specific menu. If you don’t see the posts listed, click on the Screen Options tab in the upper right and check the checkbox for Posts. Then they’ll show up. You will also see that you are able to create custom links that can be included in your menu. You can stick your static pages in there. How cool is that!
Honestly, menus have got to be the most exciting new feature that WordPress has come up with. I just love it.