These two statements are incongruous. Your first statement strongly implies that charging a 6V battery and high current is readily within your ability. Your subsequent statement clearly indicates you can ONLY charge 36/48V. Please consider that those trying to provide advice will benefit from better information provided on your part.
Given that you have 5400Ah of 6V capacity, you need to consider that in your charger selection. A 20A charger will take >270 hours of charging. This may be burdensome.
Given the circumstances, it may make more sense to charge in series; HOWEVER, it is critical that you monitor the voltage of EACH battery in series to insure it does not exceed the recommended absorption voltage significantly, and they never exceed. I would use your highest amperage 36V charger and configure the bank as 4P6S to minimize the number of voltage elements you have to monitor.
When constructing your bank for charging, ensure you use best practices as much as possible:
Wiring Unlimited is a great resource that covers many many common topics and questions relevant to DIYers. It is a free E-book from Victron Written by Margreet Leeftink. Check it out! Download
diysolarforum.com
Once you are equalizing, it would likely be best to use chargers on single 6S or 8S strings, so you can be confident that all cells in series are getting the same current.
Again, monitoring the individual 6V during series charging is very important. The highest voltage battery is your limiting factor. If you allow it's voltage to go too high, you will damage it.