With the filtered inputs, both line level and speaker level, the Polk is going to apply it's own internal low-pass filter based on where you set the "LOW PASS" dial on the sub.
With the unfiltered input, the sub will play the signal as received.
If you are using your Sony to do the bass management (which most people do), then connecting one of the Sony's subwoofer outputs to the Polk's unfiltered LFE input is the way to go, IMO.