I should add that my receiver doesn't have any auto calibration - all the settings have to be done manually.
1) Sub's Crossover Frequency to highest point just before it clicks over to the LFE setting.
2) Sub's Volume to 50% / 12 o'clock setting
3) Sub's Phase to 0 (zero) degrees
4) Amplifier sub volume to 0dB. Amp crossover frequency to around 140Hz. (Fine tune by ear once all other settings are done)
The first live adjustment on the sub will be made to the Phase control, but you'll use Phase and Volume during the process.
Set the amp to 5-channel stereo mode. Play some music with a pronounced bass beat. You will be adjusting sub volume up or down as required until you can hear the subs contribution but it doesn't swamp the satellites.
Then you will adjust the sub's phase control to get the strongest bass beat. This is the point where the sub's bass cone is moving in the same direction as the satellite so that they are in sync (AKA in phase).
Lastly, finish off with fine tuning the volume. For this you can use the volume on the back of the sub or the amp's channel volume in the speaker set-up menu. That's actually a bit more convenient because you can make the adjustments from your main seating position.
The ideal sub volume setting is where the sub contributes but without drawing attention to itself.