Nice system EJ!

I would recommend installing the firmware update on the 990. It makes life a lot easier both for setup and regular use. And a question, did you make sure the 25 and 50 Hz settings are zero on the Descent? If either is too high, this would definitely cause booming.

As it says in the Descent manual try either letting the 990 do all the bass management or use the standard 2-channel hookup between the Aeons and Descent. What you are doing is mixing the two, and as Gonk recommends it is good to avoid double sets of crossovers.

If you let the 990 do the bass management just make one connection from the 990 sub output to the LFE input on the Descent. According to the Descent manual this bypasses the internal Descent crossover settings but still allows you to shape the bass with the 25 Hz and 50 Hz level controls. Again start these at zero. You could even use a balanced connection for this.

The other option is to use the Descent crossover by doing the 2-channel hookup between the Descent and the Aeons as described in the Descent manual. If you do you need lots of long cable runs. Then you configure the 990 with NO SUB and the fronts as LARGE. The 990 will divert the bass from the center and surrounds to fronts, and the Descent's crossover will handle splitting it appropriately between the Aeons and the Descent. Again you can use still the 25 & 50 Hz levels to control deep bass and boominess.

Between you and me, I would try the first set up consistently before you give up on it. Adjusting the sub levels and settings with knobs on the sub is very tedious -- you need a friend to sit by the sub and turn the knobs and switches while you listen and measure.