1 Stirring the eggs a couple of times while the water is coming to a boil helps center the yolk and ensure even cooking. 2  When you boil the eggs make sure the water is at boiling point. 3  Cook the egg for 12 minutes for a large, 15 minutes for an extra large. Stirring the eggs a couple of times while the water is coming to a boil helps center the yolk and ensure even cooking. 2  When you boil the eggs make sure the water is at boiling point. 3  Cook the egg for 12 minutes for a large, 15 minutes for an extra large.