I think the easiest thing for you is going to be to put the miniDSP right before the sub. That’s where most of your bass issues will occur anyway, and miniDSP is pretty transparent, especially for subwoofers.
Plug the ports on the back of your main speakers, this will make integration easier and lower the distortion and bass output.
I’ve had a great deal of success with this alone.
If you wanted to take this 1 step further, put a capacitor in line with your amp. This will give you a 6 db/octave high pass filter. Use about 0.04uF for an 80 Hz high pass filter.
Of course, if you are experimenting, at each of these steps you’ll need to remeasure.
Almost forgot: Seek out the AM Acoustics room mode simulator and try to keep your sub, speakers and listening location outside the lowest room modes.