Retrofitting App to use CodeIgniter

[eluser]dcunited08[/eluser]
Currently, I am using ob_gzhandler to compress the output on javascript files, I guess custom is not the right description, per page is more like it. I did, though, like the idea of using routes because my next issue is how to use CI code within the legacy part of my application. I.E. I would like to create a view that is the header for all the pages, simple enough for the CI part (all one page of it currently) but how can I use it in the non-CI parts? I have been attempting to load CI as described in the manual for Libraries but I have yet to find how to include all the files without it trying to serve up a page. I think Pages works well for a few files but I was quickly running into the issue of altering my site drastically to work within CI. The site is primarily scripts that are interlaced together and I want to transfer over the site a little at a time, not all at once. I attempted it and then saw the htaccess path which got me up and running faster.