The danger in running with the switch on "both" is that if there is a substantial difference in the charge level of the batteries, that the higher battery will "charge" the lower battery without any limit to the current and it is possible to buckle the plates on the battery.

Someone will of course say..."Hey why doesn't that happen when I jump start my car?"
Two reasons... 1) You don't run for hours with the batteries jumped.
2) The battery cables used when jumping a car are typically longer than the cables in the boat and the clip on connections are not as low a resistance. Put simply, the short cables and the very good contacts in the switch in a boat's system provide a low resistance path, that allows a higher current to flow than in the jump the car scenario. Contrary to popular belief, when you jump your car (or truck) the good battery is not providing the cranking amps to start the dead one. It can't... the cables are too long and the connection too ratty to allow the several hundred amps that the starter needs. What happens, is that the good battery ( you all notice that things go a bit faster if you rev up the charging vehicles engine a bit for afew secs!) fast charges the bad battery so that IT can mostly supply the current to crank.

RE:"the system "retriever" mentioned is not really the best choice.it's best to be able to control all the power from batteries and it's best to be able to shut off that power."
mmmm... guess you didn't read..."a seperate on/off switch could be wired from Battery B to the electronics." When this switch AND the "main" (1-2-both) switch are both in OFF... no power to anything...except to the bilge pumps which as you pointed out should be hard wired to the batteries.

I haven't bothered doing this ( adding the additional on-off switch) on my current boat since as stated, all the electronics get unplugged... ALSO and a good idea for all... I have a heavy wire run from Battery B (the start/deep cycle one) forward to power all my electronics. At the point where this cable attaches to that battery, I have a 30 A fuse. Per stardards, this fuse is NOT to protect from the equipment over load ( that's what the individual fuses are for AT each piece of equipmemt), but rather that fuse is there to protect the boat from a short in the wire "bus". If I need to shut off that heavy feed (bus) from that battery to the helm, I just pull the fuse.