Right. Guess I wasn't clear. The idea was to do the 2nd one with the mains and 1st sub both already on so you're blending the 2nd sub with what you already did.Yes, and probably repeat both subs once or twice more too, since phase adjustments can interact.
Agreed. You may need to adjust from perfect phase later on. However, IMO it's important to get everything in the proper phase to start with and then adjust later if necessary. Adjusting peak at xover via the phase control is a tradeoff IMO of better FR for muddier bottom end. I'd prefer to get the phase correct and then lower the xover point on the sub so you leave a gap between the mains xover and the sub xover to deal with any peak. Using phase for that is usually my last resort.One of the problems with the single tone method is that you could be adding to an existing peak at the crossover frequency that makes the situation worse.
A better method would be sweep the sub and mains with REW software and adjust the phase controls for a smooth transition at the crossover.
At minimum you need to test with multiple tones above and below the crossover to be sure you're not simply creating a peak with the phase controls..