Audioino?

so I am running my project off of a rechargeable 3.3v coin cell but the project will be charged using a USB connection. the micro usb has 5 pins so I am considering using power, ground, rx, tx, reset since this will allow for charging and also allow the chip to be reprogrammed. I would like to use an UNO's ftdi chip to program my project but i hear that the UNO is a 5v programmer and it could damage my circuit. How would I allow for 5v ftdi programming? The atmega itself should be fine with 5 volts but my battery and my nrf24l01+ wireless chip probably should not go up to 5volts.

any suggestions?