The automatic Accord is far more common...prob. 90+% of the new ones sold. I'd say auto. is really "standard" for a sedan. It's also more expensive than the manual shift model, if you're talking about the 4 cyl., and more expensive to fix, too. (If you drive a stick car right you might only need one clutch change as long as you drive it. Rarely anything else craps out on a manual, unless it's abused.)

The auto. should resell for more since it costs more initially. That's the way it goes...It's also a family car, and the driver demographic leans more to the non-racer. Now the V6 coupe is a whole 'nuther discussion.

Oh, and on shifting an auto...don't waste your time, just drive it. The only exceptions I'd note is driving downhill on a steep grade and hauling a load. In the mountains, 1st or 2nd gear down a hill can save brakes, but then you have to be careful not to overspeed the engine. Also, in the rare case you hitch up to a small trailer or are carrying a very heavy load, you should stay in D3 instead of D4.