Setting Auth and Config values for a 3rd Party File Manager?

[eluser]mdvaldosta[/eluser]
I'm driving myself nuts trying to workout the best way to handle setting the config values and auth function for the CoreFive filemanager. It integrates nicely, but I'd like to have this work off the codeigniter side because I need to secure it, among other things.

It's all in the assets folder at the moment. There's not a simple class wrapper like with CKFinder that I can just load up into a CI library and instantiate... so what's the best plan of attack here? Anyone done this already? I can come up with several solutions but all of them feel like a glued together hack.