@Jonathan Galea
Can you control the Sub without fully engaging LEO? This is what you should do. Phase can be set afterwards to maximize sound (though only in 90º increments). EQ can be applied separately, it looks like.
Allow YPAO to do the first round of correction. See what happens.
Perhaps run LEO after YPAO just for experimentation. See what happens.
If you not your manual settings, you should be able to return to them with no problem.
I just want to encourage you to experiment and not rely on what MA probably intended to be used with just a Stereo Receiver with no room correction. (Just a suspicion there, but it seems reasonable.
I know very little about YPAO, but based on what he OP said and the manual, I think doubling up on LPF, for example, as well as fighting over SPL goals. To me, those should come first, then experiment with EQ and Phase on the Subs.