I have 2 12V batteries in series and I have 2 12V batteries in parallel. Currently an outboard motor charges the two batteries that are in parallel but not the 2 12V batteries that are in series.
I need to understand how to get the charging source to be able to charge the 2 batteries in series as well.

 

This topic is falling dangerously close to the automotive rule but here is one answer...

If the charging system for your boat is 12 volts, then you can only charge 12 volt batteries in parallel because two batteries in series will total 24 volts and power from the batteries will flow into your charger (actually it won't flow back since diodes block flow into the charger).

One way to charge your batteries in series is to use an AC inverter. This takes your 12 volt DC power, converts it to 120 V AC power (like in your house). Then you can plug a 24 volt charger to the inverter and charge the batteries connected in series.

Be careful that the total amperage (amps) loaded on your boat's charging system to charge the two sets of batteries plus power any accessories (lights, fish finder and so on) doesn't exceed the rating of your alternator, rectifier or voltage regulator. Measure voltage at your battery when boat is running with and without the accessories, inverter and other accessories connected. Voltage shouldn't drop below 13 volts. Check immediately after starting then again after 1 min, 3, 5, 10, 30, 90 minutes of usage. Disconnect inverter and other accessories if voltage drops with time. You are not generating enough power to keep everything charged and operating. Remember that more power can be generated at higher RPM. In any case, always check that you will not be overloading the maximum rated power of the charging system.