Normally everything except the trolling motor runs off the cranking battery but this is not to say you can't run things off the TM battery(s). The bilge pump should only run when there is water to be pumped out. Most outboards have low output charging systems. For this reason I have always recommended when installing an on-board charger that you get one big enough to include the cranking motor. Most people simply do not run the big motor long enough to keep the starting battery charged and eventually you run out of cranking power. Also remember if you have ever connected a charger to the cranking battery backwards, even for a split second, there is a 99% chance you have blown the diodes in the charging circuit.
Fair Winds and Following Seas
Bill H. PTC USN Ret
Chesapeake, Va