Yes, your prelude has an external factory amplifier for the rear speakers. I can't be positive what kind of signal that the amplifier would be expecting but it is probably just a low-level "pre-out" signal around 2-4 volts. Make sure you are not sending a high-level or speaker-level signal to the rear. A wiring diagram might help you to double check your connections.
Here is the wiring diagram for your 97 Honda Prelude: