AndrewS,

That was exactly what I was trying to explain about the sub level.

I found it has sounded better in my system to actually set the crossover on the sub instead of deactivating it. I do this via the SMS-1, but you should be able to do it with the knob on the sub. It may not sound better in your system, but again, it did help tighten up the sound in mine.

I am not sure as to the cracking noise. You may want to check your connections or perhaps try a different cable(s) to the sub(s).