The concept visualised from the birds view: 

Power supply can be a USB-cable and/or one of the named battery solutions or maybe LiPos (all batteries = XOR). The CR2032-option has later to be tested if the internal resistance of the battery prevents the use of ATMega and RFM69. When battery powered, a reverse polarity protection protects the circuit. Using USB-power and battery at the same time is possible. In this case battery is used as a backup solution. An electronic circuit guarantees a minimum voltage of 2V.

The ATMega can control the power supply circuit so if it needs 3.3V for the additional components, it will be there.

With solder bridges it will be possible to influence the behaviour of the circuit (for example: FORCE_3V3).