okay, he is right about them going back and forth, but I'm not aware of an aftermarket radio manufactured today that has dual antenna inputs....so to answer your question, use the power antenna rather than the diversity(rear glass) antenna. it's the larger plug and will plug right into your aftermarket radio without an adapter.
an antenna adapter will only amplify your signal(static/distortion and all), not increase the sensitivity of the tuner. for better overall reception, get a headunit with an excellent tuner section. sony's ssia tuner in their ES peices works very well, so does the pioneer supertuner.