Turning up subwoofer bass through factory system?

It depends on what equipment you have and what kind of factory system you have, but your best bet would be in install a bass knob, run it from your amp to the front of the car, and control the sub bass through that.

The instability could be in the amp. Make a decision on having it swapped out before the warranty expires. It's possible that the DC ground at one point is not exactly the same ground potential at another. Direct coupled amps with response down to DC, can be affected by slight differences in ground potential at the chassis of the radio and that of the amp ground. It's possible that after playing the radio, the radio itself, has a leaky electrolytic capacitor in it's circuitry or some other flaw, that causes it to begin to output this extremely low frequency, and the amplifier dutifully reproduces it. Substitute another source of audio and do the same tests... if it still does it... Make the battery negative the common ground for all ground connections. In desperation return the amp, while it's under warranty. If it's the radio turn the gain controls down at the amp (if there are any), and use a higher volume at the radio to get the same maximum volume. The flaw in the radio circuit or the system, is being over-amplified.

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it turns up both unless you have a crossover before your amp...............and i like spam lol