The autorouter just doesn't work that well. Mainly it makes some really ugly choices from both a design and aesthetics perspective.
The manual way involves a few hours with no risk of interruption, and a case of soda or other favorite beverage. Arrange the components in a logical way and then route the important wires (power, high speed, etc) first. It's like a big puzzle! At least for me...for others it might be the worst drudgery. Naturally it's not a very practical approach for something really complicated like a motherboard. You need much more expensive tools that can handle things like trace length matching.