How can you say A or B is better when you don't know where the port opens up inside the box? If it's an s-port, all the way to the opposite side of the box would be best. If it's an L-port, it depends on the the length of the port.
My sub box has that type of port, and the sub placement is your b example, box built by double07, and it pounds the lows. Only diff is' mine is sub up port back.