1996 Honda Civic bad alternator

1996 Honda Civic mileage: 165,000. My engine wasn't starting so I took it to a friend's auto shop to have it worked on. He found that the alternator was bad and the engine flooded. I got the alternator fixed but the battery still won't charge. The mechanic mentioned something about the IG wire or the L wire wasn't properly connected to the exciter on the alternator so the alternator wasn't being "told" to work. What does this mean exactly? My father and I are going to attempt to fix this but we need some help. Thanks for your assistance.