The native firmware will have no way to use the codec. In order to gain access to Rockbox's functionality you need to install it according to the instructions. It's a self-contained firmware written from the ground up, not a set of plugins designed for a pre-existing firmware.
You could probably get away with a sparse installation of Rockbox, but if you're going to take the plunge I don't see why you'd want to cripple a superior firmware (Rockbox!). Remember that you can always boot into the Apple firmware if you so choose.