Code Igniter WordPress how to handle WP templates

Dear forum users,

I’ve been playing around with both codeigniter and wordpress.
Now I would like to get these two working together using CI as front and WP as back.

But I got pretty stuck on the beginning, I’ve managed to run both togetter… But I am wondering how you are supposed to handle the templates from wordpress ?

I could easily generate a totally new site upon wordpress using wordpress as backend, tho users will not be able to change the template.

So for example in your wordpress template folder you have a header.php, which you can reference using get_header();

I’ve came up with the 2 ideas:

1. completely rewrite the WP header.php and footer (into an header/footer view), but then it wont be compatible when changing templates ?
2. created a header.php view in codeigniter, this is a php file with only one line:

<?php get_header(); ?>
This will call the WordPress header, this way my CI application will be able to handle template changes in admin panel.

But I feel this way I am not using the power of CI views for my header and footer.
I would like to implement a template engine later on, so my header and footer will not be able to use these template tags this way…

Anyone experience with these issues ?

Thanks