The folks at M&K suggested to me to trust the 990 cross over and turn off the cross over on sub.

In other words "Open it all the way up".

Why have two crossovers? Makes sense.
I did this also and found the sound more smooth. They said to experiement with the 990 cross over to what sounds best, not the sub.

Im still working on it and perhaps I will for a while.

The SMS will give you 5 different settings you can configure. While tweaking is necessary as not all material is the same, I think for the most part you can create what you need between those settings and the volume without having to keep getting up.

I think the SMS will also assist in the polarity.