It could be a few things. There is too much current going through those wires, that is why they are getting hot.
It could be that there is a short in the system that is draining the current. It could also be that the regulator is malfunctioning, making the alternator overcharge the battery. The alternator could have a bad field, causing it to overcharge all the time.
Thats a few obvious things to look for.

Sheldon