So, here are the answers to my questions:
oedipus said:
Where are the good places to put a sub?
Close to a wall is good, and in my experience, corners are the best. In this position, the sub does a good job of exciting the room modes - I'll come back to why this is a good thing. 2 subs is a more interesting configuration which I'll return to at a later date.
Where are the good places to put the main speakers?
How do these distances compare from the listening position?
Well, the main speakers are usually away from the wall, and out from the corners, so the net result is that they are closer to the listening position than the subs.
What signal gets delayed? How is the delay implemented?
So the signal to the main speakers gets delayed (because they are nearer) and the delay is implemented digitally.
So, speaking hypothetically, let's suppose I had a Velodyne sub, say a DD15, and a fancy high end an analog source, perhaps a Mark Levinson 390S; have I wasted my money on the CD player if I wish to properly time align my sub with my main speakers?
And when I was faced with that question I concluded that, yes, an expensive analog source was a waste of money, because its signal was going to be digitized (for delay) on the way to the main speakers.
merlin said:
time alignment AFAIK is the process of ensuring that the overlapping wave fronts of your subwoofer and satellites are in phase.
It's probably best to dispense with "time alignment" and think of the delay and phase dials as a way to get the amplitude response right. You might deliberately have the sat/sub signals arriving somewhat out of sync(/delay/phase) in order to get a flat(ter) response.
Now, getting back to Mr Ohm and his "phase"/acoustic law, that discussion was about the
inaudibilty of the different relative delays of different frequencies (in this case, the bass being "behind" everything else) even if the amplitude response is flat... So, getting all the frequencies "in phase" isn't a big deal.
So we have a problem. Most subs do not have continually variable phase.
Even if subs had continously variable phase, the phase cannot "advance" the signal to catch up with that from the sats (even the mighty velodyne DD series can't do this) so there will always be a time lag of the bass behind the satellites. Subs don't need much in the way of delay (phase) control because the delay is expected to be supplied by the processor to the main speakers. (Because of the snafu over bass management in SACD and DVDA, it's been pretty difficult to make those formats work in a previously installed system, until the players started doing cross-over/delay..)
Consequently they are very hard to integrate without careful positioning. The hard fact is that the majority of commercial subwoofers offer no alternative for correct alignment other than to experiment with positioning.
To be fair to the subwoofer manufacturers, they expect the delay function to be implemented elsewhere.
Even with the right tools, subs are not the easiest things to make work properly, I suspect many people have given up in frustration and "declared subs don't work"; moreover adding a sub to an analog system seems to require a substantial amount of luck, which explains why there's a great deal of variability in the experiences people report..
FWIW, undoubtedly subjectively the best bass I have heard is from my JBL subs, placed inside the satellites in the same plane, and without any form of digital processing or EQ.
Sure, but they are giant subs

They would happily drive the room from wherever you put them. However, they'd work less hard in a corner where they'd couple to the room properly and you'd get some "free" gain and that's important for smaller subs that are being expected to work miracles, and even for big subs at high volumes, you'll get lower distortion if the sub isn't working so hard.
Returning to the point about exciting the room modes; with EQ, you can have your cake and eat it: you can put the sub in the corner, and in most rooms excite all the room modes, have the fewest valleys, and get the most volume for the least cone excursion. Then you can flatten the peaks with EQ.
The other nice touch is that if you've got small sat speakers you can considerably ease their load (and hence lower their distortion) by crossing them over further up. And as the sats are putting out less bass, they are less likely to cause room boom resulting in more freedom in placement. Of course to do this, you have to go down the AV processor/Tact/behringer route and give up on analog sources - unless that source is one of the new breed of DVDA/SACD players with bass management rolled in.
Right, I'm off to "experience" my actual (not hypothetical

) DD15...