The variable phase controls are useful. They can align the drivers at a given frequency between sub and speaker.
What the dial doesnt do is time shift the sub ahead to account for its DSP/Amp/large driver latency. You need to shift it ahead of your towers in time using delay settings. The distance setting (increasing distance over physical location) helps with this.
The one stop shop to do this without manually doing latency close mic measurents is Dirac. Otherwise its sub latency+Physical distance= Avr Setting. Then you can fine tune phase with distance or phase dial settings. I just leave the dial at zero and do from behind mic position with remote while watching graphs. Geeky all the way!
Btw, SVS dials are not really useful at all in my experience. They are not accurate from unit to unit. Have to verify manually. Especially gain. Way off between units.