I responded to the same question from the OP about setting delay on the Audyssey thread, and there are just two things that I would like to add to the good suggestions above. First, it is also perfectly acceptable to run Audyssey before making tweaks in order to let it do its best to set filters (control points) which smooth out peaks and valleys in the frequency response, and then to adjust delay manually afterwards. That will not invalidate the EQ that Audyssey has already performed. You will simply be tweaking the phase controls (or delay controls in this case) to attain further improvement in the frequency response, or in tactile sensations. So, if the OP is having trouble with Audyssey undoing his pre-calibration tweaks, just run Audyssey, and then add the delay tweaks afterward.
Second, there is sometimes a misunderstanding about what any version of Audyssey does with respect to multiple subwoofers. The .1 (subwoofer) channel is a single discrete channel, and it gets a single filter with the number of control points in that filter determined by the specific Audyssey version. For instance, the filter in XT-32 has more taps (control points) than the filter in XT or MultEQ. But, in all versions, there is just one filter per channel, and all subwoofers on that .1 channel are EQed exactly the same based on their combined sound. Dirac and all other systems of automated room EQ with which I am familiar work the same way.
XT-32 with SubEQ has two sub outs. And, having those two subs outs allows Audyssey to set distances (timing) and trim levels separately for two subs, or for two or more pairs of subs. But, the only difference in methodology is with respect to setting two different trim levels and two different distances, and in giving the user more convenient control of dual volume settings. The process of EQing all subs in a system as one, based on their combined sound is exactly the same. As noted above, XT-32 has more control points than XT has, and so on down the line, but the process of how the subwoofer control points are implemented doesn't change among the various versions. They all EQ all subs in the system as one.
GUIDE TO SUBWOOFER CALIBRATION AND BASS PREFERENCES
* The Guide linked above is a comprehensive guide to Audio & HT systems, including:
Speaker placements & Room treatments; HT calibration & Room EQ; Room gain; Bass
Preferences; Subwoofer Buyer's Guide: Sealed/ported; ID subs; Subwoofer placement.