I developed this circuit board with a pogo-pin adapter in mind to program the ATmega328PB. The pads are on the bottom side and you need something like the adapter sold by PNOXI on tindie.com.
Furthermore everything is done through pio, the commandline tool for PlatformIO.
The fuse values are configured in platformio.ini. Run the fuses target to
program them to the correct values, which are mostly the defaults except for
disabling the CLOCKDIV to reach 8 MHz with the internal RC.
pio run -t fuses
To compile and flash the firmware simply use the upload target. I'm using an
Adafruit FT323H to program my chips. If you're using something different, you'll
need to change the upload_protocol = ... in platformio.ini accordingly.
pio run -t program