Adding PHPRunner to a CodeIgniter project

I have a client that has a program written in CodeIgniter.

They want to know if I can implement the PHPRunner app for them inside the CodeIgniter app. Meaning that it looks seemless to them all in one program and showing on the CodeIgniter menus.
I have figured out the menus, but keeping the same formatting and feel is proving to be difficult for me.

Anyone have any experience with this and can share some tips?

Thanks
Paul