The position of the mains is definitely better in your second diagram, yes. But the location of the sub is less critical. Assuming you have a long enough sub cable, you can experiment with locations pretty much anywhere in the room. Try to stay away from room corners, as that will cause boominess in the sound. Try the "crawling for bass" technique -- place the sub in your prime sitting location, then crawl around the room and listen for the smoothest, clearest bass. That will be the best spot for the sub. Good luck!
cheers,
supervij