If you change the sub to none, you can't use the sub output of the 990. You'd want to either leave your 990 speaker setup as it is and move the sub output cable to one of the sub/sat inputs on the sub. Leaving the mains small and using one of the sub/sat inputs on the sub will let you use the 990's bass management effectively for non-bypass inputs and use the sub's low-pass filter to control the sub's signal when in stereo bypass mode.