I am wondering will the stock converter/charger still be okay and the charging from my truck at 14.4 volts be okay since the batteries hooked in series will equal 12 volts. Who can explain why this is okay, anyone.
You obviously understand that when two 6 volt batteries are in series are seen as a 12 volt load, so I'll try to use that as a premise.
Your convertor (or truck charging system) produces 12 volts, and at some maximum current - Your convertor is likely 60 amps maximum. How much current (load) a battery represents is based on the voltage applied to it. Just opposite as when two 6-volt batteries are in series they produce 12-volts across the two, when 12-volts is applied the voltage divides across the two. The current going to the batteries is determined by the voltage applied to them.
In a 12-volt charging system, the charge voltage is normally 14.4 volts at a high rate charge. With two 6-volt batteries in series the same 14.4 volts is applied, but each battery only sees 7.2 volts.
In this example, if everthing remains static and one battery is a 10 amp load, two batteries certainly is a 20 amp load, right? But, charging systems are regulated. As they approach their current limitations, they back off on the voltage to maintain the charge rate (current) below their maximum. There are other limitations, like cable sizes and fuses to consider, but almost all convertors or vehicle charging systems will handle multiple battery strings.