The guy who previously owned my center console had set up two banks of batteries. One bank of 3 for the 36v trolling motor, and another bank of 3 with one dedicated to the outboard and the other two in parallel to power all the goodies and lights on the boat (he night fished). He had a single 15amp x 3 bank Dual Pro charger for the trolling motor and used a 6 amp Guest single bank switched manually on the other 3 batteries.
Needless to say, I thought that was too much work and would be a pain in winter storage having to keep switching the single bank between the 3 batteries. I bought one of the new "recreation" series 3 bank dual pro chargers and love it. It only has 6 amps per bank, but unless you are turning around every couple of hours after draining the batteries it should be plenty.
Here is the cut sheet for this model:
http://www.dualpro.com/media/pdf/RS2%20insert.pdf
I bought mine from "Batterymart" and it was drop shipped direct from Dual Pro when I ordered it. Cost was $160 for the 3 bank and the 2 bank for your application is $120 with a 2 year warranty (Dual Pro is a very good brand that stands behind their units). Just buy two of them and wire them into the same AC shore power circuit.
http://www.batterymart.com/p-dual-pr...harger-2b.html
Or you can get their 4 bank "SE" Sportsman model which is a 10 amp per bank charger for $381 if you don't want to have multiple chargers.
http://www.batterymart.com/p-dual-pr...harger-4b.html
The difference between the Dual Pro and most of the ProMariner models is the Dual Pro has a dedicated charger with x amps per battery. Most of the ProMariner (ok, the more affordable ones - excludes the professional top end models) use a combined amperage for the bank of x number of batteries. Some people swear by both types, some swear at both types. I have ProMariner 45amp 3 bank model in my electric freshwater boat for the local electric only lakes and have never had a problem, but it did cost about twice what the Dual Pro did. I went with higer amperage for that boat as the batteries are the sole source of propulsion and needed the quicker charge time.
Either brand will serve you well, but the Dual Pro recreation "R" series is hard to beat for a weekend angler. Both are sealed and waterproof.
Google for pricing, but batterymart is usually about the lowest and a very reliable vendor. I've been buying from them for over 10 years.