I never want my bilge pumps able to be "accidentally" shut off when my main switches are. I like to feed different bilge pumps from different battery banks so that if one bank fails or one pumps runs down a bank another is available as backup.
I also like a separate, extra, set of bilge pump float switches just for alarm purposes: I have these set higher in the bilge than the pumps....so if my bilge alarm system goes off I know (a) either a pump or bilge pump switch has failed or (b)a pump has been overwhelmed. In either case water is higher than it has ever been. An alternative might be to have indicator lamps which ignite whenever a pump does.
I added the extra alarm float switches in each bilge compartment after about 55 gallons of diesel siphoned into my bilge overnight in Cape Cod ...a fatigued fuel supply line. It wasn't enough to trigger a bilge pump, fortunately,but I might have been unpleasantly surprised had I not smelled diesel fumes the next morning. I used a spare bilge pump to extract the fuel and resued about 1/2 or more.
On a fiberglass boat I worry most about a raw water engine leak when I am underway...say a raw water hose or hose clamp breaks and water galore is pumped into the bilge. DD pump a LOT of raw water. To cover this, I use in line raw water flow detector with an alarm. So I get an immediate feedback (alarm) if raw water is lost...So now I need mostly concern myself with an exhaust leak while underway...small chance by comparison and the bilge alarm system should cover that.
No need to run bilge pumps thru the OEM breaker panel....but that's fine. Several of mine run that way, several run thru a separate house/aux panel added. I like physical wire routing diversity and power supply diversity.