1. Do you have a factory alarm or an aftermarket alarm system?
2. Dont know if this will help you, way old thread, real short but give it a read:
Problem with my OEM alarm - Honda-Tech
3. If its an aftermarket system, more than likely you are in valet mode and need to toggle out of valet mode to get your lights and such to activate you arm/disarm your alarm. With all the different alarms out there, I have a compustar and for me all you do is turn the ignition key to the ACC/ON position and off again 5 times within a few seconds and then hit the arm/panic button on my keypad to get out/into valet mode.