Yes it will definitely require some modifications to the firmware. Basically you communicate with FONA using serial communication: you send commands and data to it, and receive data from it, all through serial communication. I haven’t looked at the specific protocol, but it’s probably some sort of AT commands, which are pretty common. Honestly since I’ve never used FONA I don’t know much about the details, but a good starting point is to look at the FONA tutorial:
https://learn.adafruit.com/downloads/pdf/adafruit-fona-mini-gsm-gprs-cellular-phone-module.pdf
which contains many examples.