[eluser]Daniel Moore[/eluser]
I've taken a completely different approach. First, I designed a theme that would work both with SMF and my CI site. I don't load SMF from within CI. I don't really think that's a good approach, as it is a completely separate application.
I defined my theme directory in SMF to point to my CI theme directory. I use a layout template there from my CI, and SMF points to the same location, so they share CSS files and template files, although they use different template files for the most part. The "above" and "below" portions are common, however, and prevents me from having to make changes to multiple files should I change the layout.
You can change the theme directory in SMF's Admin panel under Configuration->Themes and Layout->Theme Settings by scrolling to the bottom and changing base path and base url to themes directory.
My 2 cents.
