Juggernaut Ships are best used as a stationary point in a Line of battle. They are useful if you want to bring as much Firepower to a Port Battle as possible or just to out-gun Third Rates. Juggernauts are, however, extremely expensive, as they all cost Burning Sea Points. Leaving these ships only being used by the Admiral of the Fleet.
This information is provided by the update that PotBS Wikia is undergoing, by Captain Vuur.