"If both batteries are on-line all the time, how do you know when one is
getting weak and needs to be replaced? Or do you replace both batteries
when voltage is marginal at the end of a flight?"

Well, that is a problem. You do not know. Everything is automatic. If you
have one battery that has lost most of it's capacity, the good battery will
do all the work. The only way you will know is when the total capacity of
both batteries has been reduced. And, then, you will not know whether one
battery has done 50% of the work and they are both down in storage ability,
or one battery is still 90% and the other one is 10%.

So, you will have to determine the capacity of each battery separately. You
could test the battery capacity by switching either off during discharge, or
even by using 2 ammeters - but it is becoming more complex once we try to
extract more information. You can also determine the capacity during
charge.

Colin