Umm...it would help if you knew what size the batteries were...that would at least give us an estimate of what the amp-hour rating for them is.... saying you have two batteries means very little... you could have two 60 amp hour, Group 24 batteries.... or you could have two 200 amp hour, 8D batteries... or two nearly dead car batteries.
What you need to do is figure out what your electrical budget for the boat is by calculating what the amperage of each piece of equipment is and how long you're going to run it for per day, on average. Once you've gotten that estimate, you can figure out how much electrical power you'll need on average...
Your battery bank should be based on your daily usage...by some multiplier...If you want to recharge every day...then make the battery bank twice the average use...if you want to charge every third day, then make it 5-6 times the average daily use... Generally, you should never run a battery bank down below 50% before recharging it...if you do so, you will drastically shorten the life of the battery bank.
Then you need to figure out how to replace all the amp-hours you'll be using up. Will you be at a dock/marina or on a mooring, or out cruising?
For a mooring or out cruising—solar, wind and water generators are some good choices of ways to go.
Solar panels are a good option, but need to be backed up by another option, as there can be long stretches of cloudy or rainy days.
Wind generators are a pretty good option, while at the dock...not so useful when sailing IMHO.
Water generators are good when sailing, but useless at the dock...
A genset or generator can be useful, but has a lot of downsides to it... as fuel is both heavy and expensive.
If will you be docked at a marina with available shore power. If so, see about getting an AC-battery charger—get a good one, with three or four stage charging circuitry, no cheap ones...they'll kill your battery and burn down your boat.
If you don't have a shore power system installed...it might be worth installing one.
Running the engine just to charge the batteries is generally not such a good idea, and should be avoided if possible. Running a diesel under a light load is a good way to give it lots of problems in the long run... they don't like being run under a light load...and doing so too often will result in maintenance nightmares.
If you need more specific advice...drop me a PM.