That's not quite it. You may have probelms with the keyless entry, as some Civics do have the keyless entry unit built into the head unit. There is an accepted method of basicaly shoving the old head unit back into the dash and leaving power to it so that it can still operate the keyless entry. Do a search for civic audio in general, as it won't be an empeg specific problem. I know in my wireing harness quest for an adapter to plug into my factory radio, I came accross wiring harnesses that were designed for civics that had the right wires broken off for a new HU and the other wires still attached to the stock HU.
This may not apply to you, however, as it's only some civics...
Matthew