Much faster than me typing...
http://www.allaboutcircuits.com/vol_1/chpt_11/5.html
Of particular interest
"We know that the voltage is equal across all branches of a parallel circuit, so we must be sure that these batteries are of equal voltage. If not, we will have relatively large currents circulating from one battery through another, the higher-voltage batteries overpowering the lower-voltage batteries. This is not good."
"With a parallel battery bank, one fuse is adequate for protecting the wiring against load overcurrent (between the parallel-connected batteries and the load), but we have other concerns to protect against as well. Batteries have been known to internally short-circuit, due to electrode separator failure, causing a problem not unlike that where batteries of unequal voltage are connected in parallel: the good batteries will overpower the failed (lower voltage) battery, causing relatively large currents within the batteries' connecting wires. To guard against this eventuality, we should protect each and every battery against overcurrent with individual battery fuses, in addition to the load fuse:"
ie: if one battery has low voltage and you switch on the second there is a rather large "dump" of power as the two try to equalize. You can cook the internals of you lower powered battery (or even cause it to overheat and explode). A smart switch will protect against this.
Cole Hersee has a good PDF pamphlet which explains how their smart switch compares Voltage and switches between the two batteries during alternator operation and in case you need to jump one off of the other.
http://www.colehersee.com/pdf/hot_feed/ ... eryIso.pdf
There's a flaw in their drawings on their pamphlet though, what it should be showing in the "Using an auxiliary battery for a start boost" section is the main battery below 12.7 (but above 9.5V) and the Auxiliary battery at between 12.7 and 13.2. The way it works is you push the button and for one minute there is a connection between the two batteries. (It does this using an on-delay timing relay) In that minute you can start your engine. The greatest difference between the voltages of the two batteries can only be 3.7V and their engineers have probably determined that that amount of time is not enough to cook your low battery. Of course if your Main Battery is below 9.5V it won't turn on. In that case you'd have to physically disconnect your batteries and reconnect your Auxiliary as your Main, then trickle your low battery separately.
I mention the separate trickle thing as you should NEVER EVER TRY TO CHARGE A BATTERY BELOW 9.5V USING YOUR VEHICLE'S ALTERNATOR! I learned this the hard way when I parked a car for 3 months, jumped it, then decided to just go for a long drive to charge it up. Your Alternator is not made for that kind of duty cycle and it will get cooked. (well, your stock one anyway. Again, I'm looking for an aftermarket one with 100% duty cycle that I can weld with and beat on. But no stock alternator that I know of can handle that kind of abuse.)