You can use two diodes one for the small lithium battery and one for the 5 volt. The small drop on the 5 volts due to the diode will not create any problem to your RCT, but it will avoid that the lithium will discharge via the 5 volts rail. The other will protect your lithium battery from the 5 volts and when the 5 volts will be off it will keep your RCT on.

Cheers

Al.