Yes, this works fine.

With regulators you also have the choice to have both regulators at the same voltage to share the load between batteries, or have one regulated at a lower voltage (say one at 5.7 volts and one at6 volts). What this will do is pull only from the one at a higher voltage thus only using the backup battery if there is a failure. This is useful if you wish to cut weight by having a really small backup battery with lower capacity. My procedure is to always turn on one battery at a time prior to each flight to make sure both are working.

I've had two occasions where the backup saved me. One when the primary battery was dead when Ilanded, the other when one of the batteries came lose during flight.

Keith B