Crossover is basically a variable filter. So if you filter something, and pass it through another filter with same parameters, you will further attenuate whatever you're trying to filter.
You can technically set the amplifier's crossover to "thru" or "bypass" and let your headunit do all the work, and vice versa. If you want further fine tuning, you can enable both.
For subwoofers, you want to use Low Pass (LPF). For full range and components, use the High Pass (HPF) setting. You want to let your speakers to perform its best in a certain range while filling the void.
For your mains, it depends on its range. High performance speakers can go further down the range. I would probably set it close to 100Hz for starters, and let the sub do the rest.
Don't forget to take advantage of your 13-band EQ to further fine tune your speakers in the cabin.
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