OK finally had some time to **** around with this again. Switched both outputs to sub and for some odd reason it sounds better. I can here the sub working even at very low volume which I never have before. I know I had it in this configuration before and can't figure out why all of a sudden it is "working" better. I also turned the lpf on the amp off and used the filter on the deck and sounds the same. I will use the lpf on the deck instead since I can change the settings there easier.
Big, when our schedules allow, I may take a ride up just to have a set of eyes and ears on it. I'd say the system sounds punchy and clear. The sub does not overpower the bass from the mids; not sure if this is ideal or not??? I was expecting that sub to be really separating itself from the 6.5s in the door.
While I was at it, I secured the magic box to the corner using some corner braces. Plasti dipped the brackets since I couldn't find black ones at the store and screwed through the carpet and into the edge of the vinyl moulding. Took a rip around town taking some quick turns and hard acceleration to see if it will jar loose and she's holding just fine. It's another option for securing the sub for anyone else looking for ideas.