I'm not sure I understand how your system is wired.
The correct way to wire a bulge pump system on a recreational boat is to run the appropriately gauged wire directly from the battery
posts to the bilge pump
controller. You never want to be able to shut off your bilge pump
by turning off your master battery switch. The controller is the only place you want to be able to turn off your bilge pump. Your bilge pump controller is usually attached to your electrical
panel. The fuse in the bilge pump controller will be the only fuse in the circuit. The controller will have an Auto-Off-Manual three-way switch. There will also be a light in the controller that indicates when the pump is receiving power.
You absolutely want a manual switch in case your float switch fails and for manually testing your bilge pump. A manual switch also provides a convenience factor of scraping a little more water
out of the bilge that the float switch does not sense is there.
Your bilge pump wire connections in the bilge must be done with heat shrink butt connectors or soldered with heat shrink over the connection. My personal preference is heat shrink butt connectors since they cannot melt like solder can. Both methods will prevent corrosion
if done correctly.
Each bilge pump should have its own controller, electrical
circuit and discharge thru-hull fitting. That's of course if your boat has more than one watertight compartment or you want two bilge pumps in one compartment...one backing up the other. All your controllers should be at the same place and labeled as to which bilge pump they control. Any other way of setting up your bilge pump system is less than optimal.
A bilge level alarm
is also a good idea. Its nothing more than a float switch set slightly above the float switch on your bilge pump that is wired to an audible alarm