Crap, I disagree with all the above posts. Put the battery charger on the pos post of one battery and the neg post of the other battery and setthe switch to both.
That is exactly how your engine charges them.
No... Electricity 101.
A low wattage charger doesn't care one bit which post it is connected to. There is no magic that happens by connecting to each battery, and in fact, unless you also merge them with the battery switch, you are only going to be charging the one connected to the positive terminal. The other isn't going to get a single electron. (there are advantages in high amperage draw applications to doing what you are talking about, but not for a small charger)
The capacity problem isn't really a problem, as lead acid batteries have a relatively consistent relationship of voltage to capacity. Lets say both batteries are at 12.5 volts, they are both at 50% capacity. Doesn't matter how big the battery is, for the system to get to 12.6 volts, BOTH batteries will need to have charged enough to get to 60% capacity... In other words, if one battery is 50% larger than the other, it will also receive 50% more of the chargers output.
A charger won't kick into trickle/float mode until the voltage of the entire system is around ~13.4. There is positively zero chance of that happening if one battery is discharged to some significant percentage and the other battery is fully charged.
