I am not positive, but if you call Crutchfield and tell them that you have a 2011 Elantra and tell them you are interested in upgrading/modifying the factory stereo, they'd probably tell you on the phone what needs to be done (not detailed, step by step directions, but a rough idea) assuming that they have wiring schematics or a diagram of the Elantra with and without the factory navigation system. I plan on putting an under the seat sub in mine in a few months but I'm going to leave that up to a local guy who's been doing custom car audio for years and years. I am sure he has the resources or smarts to figure it all out without any problems and for $75 in labor I'd rather have him do it then sweat and curse for hours trying to do it myself.
I think that someone said in a recent thread on this forum that the Elantra's external amp is located in the trunk on the passenger side underneath the rear deck but I haven't looked myself. If it is there you could probably tap into the signal there or just remove it all together and replace it with another amp. I do know that all the speakers in the car are 2 Ohm though so you have to make sure you match resistance loads unless you plan on also replacing the factory speakers too.