i do a lot of time alignment or adjusting the phase.
the first thing i do is to record with a high amount of attention to phase issues between the mics and the sources.
when i'm done with micing the kit carefully and everything is recorded well, i begin to check phases between the mics and then i try to time allign, so that it makes sense to me.
my kick and my snare end up with multiple mics recorded.
although i was really careful with checking phases before recording, i can see that there is some different 'wavemovement' in the files.
best example is my snare, it has three mics, two on top and one on the bottom.
the both on the top are really close to each other in the waveform, but not really identical in their 'ups and downs' - i time allign one of the top mics to the other till it fits perfectly, check with phase reverse on one mic, voila really thin sounding snare and most important: thinner sounding than before the time alignment.
then i time align the bottom mic to the top and most of the time i end up with them to be in phase.
it's been years, that i just had my phase reverse button pushed on the bottom snare mic - i time align, till they are in phase or completely out of phase, but this 'rule' to just phase reverse the bottom mic to the top does not work for me - you'll never get the max sound out of it.
for me this is the first step in time aligning the drums: multiple close mics adjusted to each other - but maybe this is not what you ment, for me this is the foundation for the 'great time alignment' to other mics like the overheads.
most of the time i end up to time align snare and toms to the overheads.
my room mics (one mono, one stereo) stay where they are, phase adjusted to each other and to the overheads.the kickdrum is not that easy to fix, most of the time i adjust it to the room mics, cause these do not get that low cutted like the overhead mics in the mix.
i think i missed your question in time aligning all mics to each other, with one starting point, but for me works the following:
close mics to overheads - yes
room mics to overheads - no
everything to room mics - no
drums are about space and this is created by delay between close mics and room mics, but this delay has to sit right.
if you don't have room mics, i wouldn't time align the close mics to the overheads, just check phase between them.
it all depends on the recording, if the micing is done poorly, you won't get the pieces fitted, but recorded with some knowledge of what you're trying to achieve, time aligning will be you friend!!
long story short - try it and decide what's sounding best for you, for me it is the above way, but that's just me after recording drums for 10 years now.
who knows what's next.
cheers,
alex