Hacking hex bot to make a battle bot any suggestions

I'm making a battle bot using hex bug scarab xl. So far I think that since it already has an IR controller that I'll just mount it to the arduino esplorere I'm going to use for the other modifications. Mounted on the scarab will be an arduino. Is there a way I can just solder wires from the digital pins to the motors that way i could rewrite there controls? Would that screw up the whole thing? Any suggestions will help thanks.