I am not well educated on this topic but since no one has 2-cent'ed up yet, I can tell you what is installed on my Carver which has 5 batteries. I have 2 main 12 volt batt's which provide for starting, windlass and 12 volt systems; they are on a 2 batt switch and charge by either the dual bank or engine alternators. I then have 2 golf cart 6 volt batt's in series (which makes 12 volts) on one switch which provides solely for a 1000 watt inverter which powers media i.e. 32" flat panel tv, dvd, wifi router, laptops and cellphone chargers. These 2 batt's, even after extended use have never run down even with full load (which I find incredible, so maybe the hours are double per your original question (?) ). Our fifth 12 volt battery on it's own switch is dedicated solely to start the generator.
While I do not know what would be best for your windlass question, perhaps I can extrapolate that (2) 6 volt's may give you more usage hours of lower power items, rather than the higher cranking amps needed out of a 12 volt to power a windlass or starter, especially considering the heavy AWG cable that's necessary to power a windlass (through the solenoid).
Prior boat: 1999 Maxum 2400SCR (I loved that boat but the wife made me get bigger). Current: '96 Carver 325 aft cabin.