Typically the bilge
pump should be wired as "always hot". Meaning if the
battery switches are off the pump still has
power applied.
Most modern
panels have a seperate circuit set up for this and "memory" circuit for
electronics that require it.
My pump is on a totally seperate fused circuit not connected to the dc panel or switches in any way. Both positive and negative go straight to the
battery bank with the bilge control panel in series on the positive side.
However, no problem with the negative going to the engine ground.
But, does your pump
work with the battery switch set to off?