The mtx thunder is a 4 channel amp. 4 channels can't be bridged to 1 speaker. You can only use one side of that amp to bridge your speaker. Unfortunately your now only using half your amp.
Take both positive leads to the positive of the amp. Both negatives from the sub to the negative of the amp. Utilize the bridged output connections. This would present a 3 ohm load which would be around 100 watts rms (rough estimate)
It is actually in the controller, if you turn the remote all the way down and press on the controller until the bass goes off, you will be able to turn the bass up and down with the remote, mine worked but stopped after a month, I tried adjusting the amp but then I noticed that if I wiggled the knob on the remote that it would work, I mashed mine until it worked again and velcroed it to my console sonibcan get it on and off easily.