All of the cubes should be set to small then connect the sub by RCA. Bose cubes are tiny and that is where your midrange is going - more of it should be directed to your sub which is why you need to assign your cubes as 'small'. Also, make sure that your sub isn't controlling the crossover point - you should set it as high as possible and the amp will decide the crossover point.
To run a sub from the speaker points of your home cinema amp, you would need to connect it to all five channels and the amp isn't really built for that & I think your problems are coming from there.
With stereo amps, connecting the sub to the speaker sockets is probably the best way but with multi channel, it's difficult and messy - don't do it.