Chuck I wanna make sure we're talking about the same thing first:
"Onboard chargers" are just that, battery chargers that are built for and mounted in the boat. They are hooked to the batteries (usually via ring connectors screwed onto the batteries posts) and then when you are done fishing you simply plug the chargers powerchord into an extension chord and it charges like a regular charger you have tucked away in the garage. They simply negate the need for carrying extra chargers and fooling with them at the end of the day when you put the boat away, you just plug an extension chord up to the onboard and go in for supper that I'm sure your wife has ready and waiting!?
For your 2 battery boat you would want a "dual bank" charger which has circuits and leads for 2 batteries. Most onboards are available in 5, 10 and some even 15 amp (per bank) ratings. That being they charge each battery with that rated amperage. Some are simply rated at say 10 amps and then that is split so that each battery is charged with 5amps (if it's a 2 bank sys, if more or less banks you simply divide the total amp/output by the banks... 10amp charger, 3 banks = 3.3 amps per bank/battery) Most of them are automatic and lets say one of your batteries is only discharged 50% while the other is 80% discharged. The better "automatic" chargers will charge 5amps to each battery, then when the 50% battery is fully charged, that bank shuts off and then the full 10 amps goes on to charge the remainder of the weaker battery until it's fully charged then the unit simply shuts off or even better, they go into "maintainer/float" mode which keeps the battery fully charged but not overcharged.
Another type of charging system ("run n charge", "power charge" etc...) actually requires the use of a larger outboard motor with a built in alternator/charging system like found on say a 4 or 6 cylinder outboard. These only work when that motor is running. I'll use my big boat for example (XB21 Allison with a Mercury 225XS outboard) has a 60amp alternator. That alternator keeps the cranking battery hot/fully charged quite easily. Well I ordered my boat with the "Stealth system" which contains an automatic electronic "brainbox/system" that seperately monitors each bank. It then splits the power/charge from that alternator to actually keep each battery fully charged. So when I'm making runs between spots I am actually charging my trolling motor batteries in addition to my cranking/main battery! Makes it nice as it negates needing to plug in the "onboard charger" when I travel to some remote places that don't have power sources. But again, this isn't really an option on a small craft unless you have a gas outboard with a sufficient charging system in the first place.
Clear as mud?
HL
I have the rather simple and "relatively inexpensive" onboard chargers from BPS on both of my fishing boats. I've had no problems with either! I have a bud that runs a local battery shop in town and he's always recommended NOT charging marine batteries with more than 10-12amps MAX as he says the bigger chargers just overheat the batteries to fast and cause them to die early. I realize some guys need quicker charge times if you fish 12-15hr days and are right back at it before dawn the next day. My answer to that is the "Stealth system" like I mentioned above, your troller batteries wont be drained at the end of the day so a slight "topping off charge" is all that might likely be required and the less powerful chargers will do that easy.
On my 16ft Lowe 160 with 50hp Erude I have the 2 bank:
http://www.basspro.com/Bass-Pro-Shop...SSSELL_PRODUCT
On my 21ft Allison/225XS Merc I have the 3 bank:
http://www.basspro.com/Bass-Pro-Shop...CROSSSELL_DEPT