There are a LOT of variables to the Polk document. Saying not to use the sub out of a receiver is a gross oversimplification of a POSSIBLE problem. Right off the bat I noticed that both of my Denons (1801 and 1803) do send bass to the sub in Stero mode. Second not all subs force you to use the built in crossover. My Athena and Energy subs have a cross-over bypass mode. Third the graph at Polk's site shows a ragged frequency response because of interaction between the two low-pass filters and the satelites. Cross-over slopes are always a compromise there actually are conditions where higher rate slopes are desired. Without mesurements there is no way to speculate as to what the resulting sound will be. Fourth, using high-level (speaker) inputs to drive an entire speakers system negates the benifits of bi-amping (everyone with an active sub is essentially bi-amping) - when your receiver clips for any reason, in the treble of the bass, distortion (IM or HD) will be realized elsewhere in the audio band.
The document does have merit in that it points out a possible shortcomming to using the sub-out jack.
Check how your receiver does bass management in stereo and measure the results to be sure you are not having this problem.
Hope this helps.
I would first set the speakers on small for the surrounds and if you have small speakers on the front,set that to small as well(if they are over 8" woofers,leave them on large).Then set sub setting to ON.Then on your PB 10 set the crossover to LFE(I have this sub and for a 150sq feet room its great.).This bypasses the subwoofers xover built into the powered sub.Then I would adjust the output level on the sub to your personal taste.But don't be surprised if you need to adjust the level on the sub depending on what you are listening to.I have the sub level on max at the sub,but I adjust the level on the reciever remote depending on what I'm listening to(movies or CDs or radio.)