Always sounds simple at first but depends upon your current set-up. Do you have one or two batteries, best to have two batteries with a switch unit and a device to control the charging of the batteries so that they are charged as needed rather than both being connected via a simple switch and then have danger of a bad battery killing off the good battery by sucking the power.
If connecting auto bilge pumps consider a good practice of having a circuit that is always on and a circuit that is switched on. My meaning is a circuit that is always on that your auto bilge pump is connected to and has a switch on the console for on but isnt dependant upon the battery switches being in the on position. Does that make sense, that way you switch your battery main switches off when leaving the boat but activate the auto bilge pump on switch on console if leaving in water for a length of time, that way you dont have anything else powered only your bilge pump. And when you dont need your auto bilge pump on if vessel is dry and out and about you just switch the console button to off position for your auto-bilge pump.
So for example my electrical set-up is routhly like this, twin battery bank with main battery switches and the battery charging unit, two circuits being a always on circuit and a switched circuit. A positve bus with fuses for always on circuit and a positive bus with fuses for the switched on items and a large negative bus for all the neagative feeds.