On my '88 boat, there is a lower panel that provide "master" controls for the bilge pumps. The panel is in the same box as the master battery switches. Located almost at the floor, right side of the helm. It also contains master power for the fridge in my boat). One half of the switches go to the right battery bank, the other half to the left bank. You (or rather, I) can shut off bilge pump power from here.
UPDATE: Here is the scenario I think you wish to achieve....
Lower/master switches off = no power to bilge pumps fwd or aft
Lower Master switches on/Overhead panel switches on: Power is available to pumps but the three way switches at the helm station are the last point of control. They are set to either Auto, off, or manual. If in auto, pump will come on when its float switch indicates too much water in bilge. The other two positions should be self-explanatory.
I can't remember exactly now but I think overhead switch in can be off and pump will still operate. If that's wrong, I will drop this paragraph.
Joel Albert, Potomac MD
"Charlie B" - 1988 32' FBS
Twin 318's/FWC/16x15 nibral props
docked Deale, MD