Millercarbon, my suggestion is this: Once you have placed the subs, first adjust the gain, then the frequency, then the phase on the sub amp. Expect to cycle through gain-frequency-phase several times.
The word "timing" seems to me to imply "arrival time". The ear/brain system is not very sensitive to arrival time in the bass region, but it is sensitive to decay time, because decay time translates to frequency response in the bass region. Let me explain:
Because speakers + room = a minimum-phase system at low frequencies, the frequency response and the time-domain response track one another. When you have a time-domain problem, you either have a peak or a dip. The good news is, when you fix one, you simultaneously fix the other. So bass traps reduce the decay time and thereby fix the frequency response along the way. Likewise when a distributed multisub system fixes the frequency response, it also fixes the time domain response along the way. Peaks take longer to decay into inaudibility than the rest of the signal, which is why they make the bass sound "slow".
Back to "arrival time" for a minute. I read an AES paper several years ago where they played signals of less than one wavelength at bass frequencies through headphones. The listeners did not detect any sound. They could not detect the presence of bass from less than one wavelength, and had to hear multiple wavelengths before they could detect pitch. This implies that relatively small timing differences - "small" relative to the wavelengths in the bass region - are not going to make an audible difference in and of themselves.
But in the bass region, the ear actually has a heightened sensitivity to differences in sound pressure level. This is shown by the way equal-loudness curves bunch up south of 100 Hz. A 6 dB difference at 40 Hz is subjectively comparable a 10 dB difference at 1 kHz. This is why we can hear the bass so much better when we turn the volume up. This is also why it takes so long to dial in the correct gain setting on a subwoofer amp - if we're off just a little bit, it's distracting. Finally this implies that the subjective improvements from smoothing the response in the bass region are greater than we would think simply from eyeballing before-and-after curves.
So I think that where the phase control makes an audibly significant difference ends up being in the frequency response domain, especially in the region where the sub is blending with the mains. I believe that the correct phase control setting is the one that results in the smoothest frequency response, but this is found in conjunction with the gain and frequency controls. They all work together... gain makes the biggest difference so we adjust that first, then we adjust the lowpass filter frequency, and then the phase, and then we cycle back through fine-tuning at least once.
Imo, ime, ymmv, etc.
Duke