Room acoustics play a big role in imaging and soundstaging. I had a similar problem where the left speaker sounded a tad bit louder and shifted the image ever so slightly to the left. This effect can be caused by cancellation of waves from on one side and/or reinforcement of certain frequencies on another side. Sound in normal rooms takes time to decay. This leaves room for constructive or destructive interference to occur. For instance, if your speaker plays a note and your room plays back the same note 180 deg out of phase, there will be cancellation. Bad bass can have a detrimental effect beyond sounding boomy. It can smear the imaging of your system, ring in your room for an extended amount of time, and excite room nodes and multiples thereof. Integrating a sub is definitely a challenge in any system.
Considering your large room and smaller sub, corner loading it would be a good idea to decrease distortion and increase output. What freq did you decide to set your XO at? How did you determine the phase to set the sub?