Without knowing your room lay out or your equipment I would guess you have a big time phase issue with your mains and subs as a result of placement. ie lots of cancellation of LF sound waves. I would also not recommend running the full mains + sub. Your asking for uneven response across the band and loads of intermodulation and harmonic distortion to muck up the upper range in the mains. Ouch.
I run my mains full as well and spend days moving subs and experimenting until I found the spot where they blended best with the mains. It doesn't sound like that spot is where you currently have your sub. And I bet you are sitting in a trough node.
As an alternative I would cross the mains as low as you can say 40hz and then try moving the sub around. Also take a tape measure and try to get the mains equidistant from each other and the main sitting position. Toeing in makes them brighter while straight ahead is better for imaging so check those out.
I have an Svs Ultra as well as 2 600s and 2 500s though my brother has carted off a 600 for now. The EPs are better performers with more output so if all else fails consider selling the SVS or just buy an ep500 and go the dual sub route. They actually blend well together because of their close tuning points.
