Id say try and leave the oboard PEQ "off" if you can. Leave the crossover where it blends best with your mains. Gain and level, id say if your receiver works on a -10 to 10 scale start with your LFE channel at around -3 to ensure you're not sending a clipped signal from the source. Once you get everything nice and flat raise the gain on your sub amp to level match with the rest of your system, or calibrate it as hot as you like (I like 5db hot
) and you're set. I found that after getting things flat I had to raise the volume on my sub to compensate for this.