In the 2001-2004 Honda Civic they are white/blue lock and white/green unlock and they are neg. (-) trip, about a 250mA 1/4 sec. pulse, most remote starts and alarms will have at least that, and they can be found in a gray plug above the drivers kickpanel.
If the remote starts works if you put the key in the ign., [without turning it on] but will not work if the key is not in the ign. then you have a transponder key immobilizer, it turns off the injectors, if the key is not in the ign., you will need to get a bypass mod. what is the model and year of your car