The two small wires are positive and negative. Most are color coded and if it's a OEM part, the negative will be the same color as the group of smaller wires connected to the negative battery cable. Each manufacturer uses different color codes and for instance, Kawasaki uses black with yellow stripe. The other wire will go to the positive side. If the coil doesn't have wire coming out if it, it may have a + or - sign by the terminals. In actuality, it doesn't really matter which way you hook it up because a coil doesn't really care which way the electricity travels. It's the collapsing magnetic field that creates the spark and not the direction or movement of electricity.
