I need a bit more context to understand the sentence fully. ...belay (stop) that fiddle faddle (nonsense) and jog the Loo!
To "jog" is to "push or nudge something gently", and the only "loo" I know of is the English slang for "toilet". It is possible that "loo" has another, nautical definition, but I'm a sailor and I've never heard of it, unless it is to do with the word "leeward" which is pronounced loo-ard.
In the Patrick O'Brian novel "The Letter of Marque", which is part of the Aubrey/Maturin series of books about the British Navy in Napolionic times, there is a situation that may explain this unusual reference.
Dr. Maturin enters a small boat to be rowed to shore after the ship he is travelling in founders on a sand bank. Water starts to come into the small boat and one of the sailors calls out "Jog the loo". A friendly sailor leans over and "briskly works the pump-handle up and down".
I therefore assume that "to jog the loo" means to work a pump handle to get rid of water. Not unlike the action in a toilet where the slang reference to a loo is made.