Where is the Ground?

So Grady White have just let me know that all the negative/ground wires should be going though the black wire so labelled. This is not the case - someone somewhere has created a link between the engine earths and the 'house' earth. AAAAAUUUUGGGGGHHH
 
Grady White Marlin 2006. I have disconnected all the ground wires (but not the engine earth) from the battery,
Have you disconnected also both engine cables from house battery, the thick ones?
You need to disconnect them too to exclude that your outboards act a ground if your boat is in a slip, if on a trailer then not.
If pumps still work if all cables from all batteries are disconnected then your problem becomes really wired.

Is your Marlin in the water or on a trailer while you case problems?
Where are your batteries located? Near the transom or somewhere midship?
but it seems that power is sneaking back from all my devices through the engine cables rather than the main negative.
This is normal as boats have a common ground for all -12V cables and -12V is linked by battery poles jumper cables and -12V bus bars/bolts.

As i wrote before, your engine cables may be too short to reach the electronics compartment where the batteries are (if it's midship).
So there is either a crimped joint (unlikely) between -12V engine cable and the bus bar under your dash to make -12V cable longer.
Or near the transom (probably near the battery switch) is a -12V bus bar where -12V from engines and at least one thick -12V cable going to to batteries are connected together.

Chris
 
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