Another option is to use a Velodyne SMS-1 with a power amp to replace the subwoofer plate amp.
That's a possibility but remember the DD has a 1350 watt amp and EQing a sub down to below 20hz requires exponential amounts of power.
My Eureka moment actually came when I selected 'small' for my front speakers (even so they are BIG floor standing speakers) and send everything below 50 to the sub. Not sure WHY it sound SO MUCH better, likely because the receiver does not have to deal with all the heavy lifting for the low octaves. Now I even run my Nautilus 804 as 'small', the 18" in sealed enclosure driven by LT1300 (ICE design) sub amp does the heavy lifting.
You weren't alone and may have been the impetus for the now twelve year old Velodyne Plus software redesign. The Plus Auto EQ now produces an improved and stunningly unnoticeable integration during the approximately twenty minute optimization cycle without any adjustment of the main speakers.