My understanding is this...
Having the auto zero box ticked on the Garmin head unit allows the power meter to zero itself without going through the manual "calibration" zeroing process.
So if you have a Quarq...
And the auto zero not selected..to zero the meter before you ride you must go through the menu the the manual zero "calibration" section...and allow the Quarq to zero itself...it returns the zero offset value to the Garmin so you can look at it. If you want to rezero duringa ride you have to stop and get off the bike and do the same thing again...you can also do it at the end of the ride to check how much the zero has moved around...which tells you if your data is consistant.
With the auto zero selected...you just back pedal at least 4 times and the Quarq zeroes itself...you can do it off the bike or on...any time you back pedal 4 times it rezeroes...this is what I do. The only thing is when you back pedal the Quarq doesn't return the zero offset to the screen so that you can see what the zero is doing...this isnt a big deal if you trust that the Quarq is working correctly. When I first got my Quarq the zero took a week or so to settle down and I was back peddling all over the place. I think the key to good data with the Quarq is to regularly zero it on the ride by smoothly back peddling.
If you have a Powertap...
Auto zero not selected...same as above..go through the menu.
Auto zero selected...the PT auto zeroes itself every time you free wheel...this is what I do. This setup is simple and really reliable and it just never misses IMO.
IMO the reason why the Quarq can't auto zero on zero cadence like the PT is because any pressure on the pedals even with no tension on the chain/no torque on the spider can still produce significant readings on the strain guages...when you back pedal the Quarq reads the strain signal as you back pedal and uses some sort of average.
When I got my Quarq I ran the PT as well to get a feel for how the Quarq behaved and to work out how to zero it best.
Sam