I use the app for both my SB 3000 and only sett the volume to -20 for one and -19 for the other, as well as giving each sub a name so I know which one I'm adjusting. Otherwise the other settings are to their default values. These subwoofer levels gives a trim around -10 in the receiver after running Audyssey.
One way to get to default values is to use the "reset" function in the app, in case you've been messing around and forgotten what you've done
And then set the volume to correct value again.
If you later wanta to experiment with the PEQ that your subwoofer has, then the app is a must, especially if you have two of them.