Isaac-
Most isolators are diode-based. Lots of them look like little audio amplifiers, with cooling fins. They are automatic, in that they allow both battery banks to charge when the motor is running, but then the diode prevents current from flowing out of the starting battery to power a stereo or other accessory device. The isolator is designed to keep your cranking battery topped off, so when it is time to go, you can.
A Perko switch is really only a switch, yet a big one. They are not automatic. Perko Switches require thought, and there are "a million" different ways to wire a dual battery system... So many, we should skip that part of the discussion for now. Again, the thing to remember and understand is that Perko switches rely on YOU to make sure the electrical system is being charged and discharged properly. Run one battery dead while listening to the stereo, only to remember that you did the same thing to the OTHER battery the weekend before is not fun. Accidentally switch the Perko to OFF while the motor is running, and you will usually fry your voltage regulator.... One last time, the Perko is not automatic; it replies on you to make sure you do the right thing.
Your isolator is PROBABLY set up so that you have the starter motor, and the other boat-related circuits tied to one battery. Then your stereo, any BLING lights, etc. would be tied to the other battery. You run the stereo dead, and you are okay, 'cause the starter motor is going to crank over from the starting battery. Once running, the alternator will provide almost all the alternator's charging juice to both batteries.
Notice I say "almost all" the charging juice will go to the batteries?????
A diode-type battery isolator makes you pay a price for the automatic operation. A diode will drop your charging voltage by .7 volts. if your alternator is putting out 14 volts, your batteries will "see" 13.3 volts. The biggest problem with diode based isolators is this very fact. Your batteries never receive the full charging voltage that your alternator can deliver.
An Automatic Charging Relay, (ACR) like the Blue Sea Systems item that Bruce Mac posted above is wired basically the same way, but uses voltage sensing to detect a charge. When it know for sure a charge voltage is present, it closes a switch, (relay) that allows both batteries to charge at the full charging voltage, again as Bruce Mac points out.
I put the Blue Sea Systems 7610 in my boat this year. I am still watching and learning, (I even re-read some stuff today to make sure we were really doing the right thing with it) but so far, I think that using an ACR, (from Blue Sea, or from any of the other guys who are building them) is the best device to have. I do not have a battery switch, and do not want one. But back to your original question, they are different, and they are not the same thing.
Check to see if you can find a part number or model number for the isolator thingie you have. If it is diode-based, you might want to addd an ACR to your upgrades list.
Phil
Kicker
(Message edited by philwsailz on June 29, 2009)
(Message edited by philwsailz on June 29, 2009)