I did this last year on Dolce Vita.
We originally had two equal house banks of group 31D batteries
at 97 amp-hours each. I paralleled them into one big house bank,
and added a smaller, dedicated starter battery as the other bank.
At the dock, charging is provided by my Xantex charger, which has
multiple charging outputs. Although it can handle three banks, I
only needed it to do two because the paralleled batteries look like a
single batery to the charger. Since the charger can only do one type
of battery, I had to use a gel-cell for my starter, same as the
house batteries.
Under way, charging is provided by the alternator to whatever bank
is selected. Normally, I always use the house bank for everything,
even starting. The dedicated starter battery is strictly a backup
in case we drain the house bank.
This arrangement has worked pretty well, but I plan to add a charge
combiner that will automatically charge both batteries regardless of
the position of the battery bank switch. It's made by
Hellroaraing Technologies:
http://www.hellroaring.com/marine.phpHope this helps. Nigel Caulder's book is really the definitive
treatment on marine electrical systems:
Boatowner's Mechanical and Electrical Manual: How to Maintain, Repair, and Improve Your Boat's Essential Systems
You should get a copy. Its available at Amazon.