I am pretty sure that the SB-1000 Pro does not high-pass filter the LINE OUT. The sub's low pass filter frequency only affects the sub.
What SVS means in their manual is that you would set the sub's cross over to where your speakers have their natural roll-off so the speakers and sub have a matching -3 dB point. This is where a measurement mic really helps with the sub integration. Without the mic, you need to lookup your speakers measurements (I forget what you have, are they reviewed here or Erin or audiophile?) and ballpark the match. What I then do is turn the sub volume all the way down, play something with decent bass (there's some spotify playlists for this, if you need one), then slowly turn up the sub while sitting in my spot until I definitely hear the sub in the mix. Then turn it down a few dB until it is not clearly in the mix. I'm sure SVS has recommendations too. This is where the BT app really helps, as you don't need to keep running across the room.
For unbalanced inputs, I think the low gain 2V output is what you want when driving your amp and sub. I would try it this way first with the amp's volume turned up to a high level.
If that does not work out for you, you could do the speaker-level input to the sub and use the amp's volume control.