The problem you will have regardless of flooded or AGM batteries, is that your standard Yanmar
(usually Hitachi) alternator will have an inbuilt automotive regulator
which is fine if all you want to do is charge your start battery
. The minute you start using your batteries for deep cycle type use, that alternator / reg system will never fully charge them...and they will have a short life.
IF you are going top get AGM batteries, I would advise that you have your alternator modified to remove the internal regulator
, get an external regulator from Xantrex or Balmar
or .... and set it up properly with your alternator size and battery
bank size programmed in to deliver the right charge curve for your system.
Your batteries will be well charged, last longer and your alternator won't burn out.