Glad to hear you have bought a Giant Power charger and it has successfully charged your new battery.
The two old batteries are not recoverable as they have been in a discharged state for too long Please do not even consider trying to revive them as due to the time they have been in such a low discharge state the internal chemistry will have changed making the batteries very unstable if you attempt to recharge. You were lucky they did not cause problems when you did a fast charge. Disposal is the only option you should now consider.
As other have said you do need something actually on the boat monitoring the battery voltage and warning you when it approaches the recommended low state. Modern batteries seem to recommend 3.5 volts as the safe limit and I have used this on my Sea Queen without problem. I can actually see the individual cell voltages on a screen on my TX and as soon as the voltage nears 3.6v on any cell I bring the boat back a slow speed as the voltage drops very quickly once the cells are depleted.
Many modern ESC are LiPo friendly and offer a set up you can set to the recommended cut - off, they also reduce the power when the voltage is too low. There are also warning devices you can fit that emit a loud noise to warn of low voltage. They work fine but may be difficult to hear at a distance in a noisy environment.
At full throttle using an 11.1v LiPo and drawing 27amps my Sea Queen lasts between 15-20 mins so you could use a stop watch to monitor your time on the water. As watts is the product of the voltage and current, using 7.4 volts would result in higher current draw and a shorter run time.
Another useful piece of equipment is a Wattmeter that will measure your current draw whilst you hold and run the model in water. This will give you an indication of the max draw as the prop will draw less current when in motion.
What motor and prop do you have installed?