I don't think it's critical; i'd use 1 at 3.9 or 4 volts while the other is charging
but in general, it's recommended to let batteries relax half hour after charging before you put them to use
I use some 10 batts in rotation.
charged ones are lined up on my desk in order.
FIFO; (first in first out)
and there's a line at my 2 dual bay chargers
as a result batteries systematically get relaxation time, because, they've been sitting in a line