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.
Good luck
Alan