From the factory they had two cables running from the negative battery, one to the MPEM, one to the block at the starter.
For some reason in my boat the MPEM ground runs to the starter, then the other one runs from there to the battery, so there's only one ground wire on the batt in my boat. Never saw a reason to change it, but if you don't remember having two wires going to that battery, it may have been that way on yours too.