Unfortunately the alpine processor is not a simple plug and play, it requires 8+ hours of initial tuning andeven over a year of tuning, it will still sound better day by day. That being said, do not rely on the autotune, its not very good. You need to go manual and set crossover points properly along with manual time alignment and EQ. I can walk you through it if needed.
Thing about autotune is that it will either lower or boost frequencies depending on what it deems missing. Usually get really bad bass boosts when you let units autotune and introduce a lot of distortion to the amps at higher volume levels