When they're tied in parallel the voltage is forced to be the same. You have to disconnect them to read different voltages.
What you probably want to be looking at is STATE OF CHARGE. You can do that by measuring the specific gravity of the banks. (Unfortunately that isn't a "hook up a meter" job. Fortunately you don't have to do it very often - monthly might be about right - to detect a problem before it gets bad.)
You could also compare the currents in the wires to the individual banks. But you have to be careful with how you do that, because very small differences in resistance in the wiring and instrumentation can massively unbalance the currents between the segments of the bank.
Also: Measuring current is an expensive proposition because you have to buy and install a shunt in each branch where you want to measure current. And the current differences from battery pathologies tends to be small compared to the operating current - until a pathology gets so bad that the only thing to do is pull out the ruined cells and replace them.
So I'd recommend that you go with periodic specific gravity measurement and leave it at that. Much cheaper, gives you an earlier warning, and you can combine it with the periodic check of the water level.