I will make this simple as possible.
For charging your "Battery bank" it does not matter if you have a row of 12 volt in parallel. Or two rows of six volt in serries/parallel. or a hugh 3,000 pound Fork Lift battery, or ________.
Electrically you have a battery. Now the amp hours will vary from one "Bank" to another (And by the way I've used that fork lift battery) but you charge them all together as though they were a single battery.
Exception.. If there is a problem. THEN you separate each 12 volt set (Either each 12 volt or each PAIR of six) so as to isolate, But otherwise treat them as ONE BIG battery.