depending on the wire size, you may need an extra line to the battery. once the amps get so high you have to either replace the cable with a thicker one or add a second. so this now gives you the option of maxing out that controler, then adding a second controler and panels to it.
if you look on the wires themselves the Gage of the wire should be written on it and that will tell you how much amprage that wire can handle. so your system you have now, you can only put two 24V panels on it and the controler will be maxed out because it can only handle 100 volts of input ( the short circut voltage of the panel that is used for this ) so if thoes cables actualy go to where you suspect you could put another one of thoes controlers in and two more panels. as you go larger in controlers the price gets more expensive like crazy.
there is also the possibility that who ever installed the solar system didn't realize there was a already installed system, or that stuff wasnt in the right spot for them, so they ran whole new wires for the install. I would ask the dealer whats going on and see if they know