Okay #Nantonos, that makes good sense 
I found in the AVR documentation, that the -p flag for the 16u2 is 'm16u2', and I've connected to the ISP header for the 16u2.
I have changed the terminal command to:
avrdude -p m16u2 -F -P /dev/cu.usbmodem621 -c avrisp -U flash:w:HIDUINO_MIDI.hex -U lfuse:w:0xFF:m -U hfuse:w:0xD9:m -U efuse:w:0xF4:m -U lock:w:0x0F:m -b 19200
This all seems right to me, but I get an error when I try to flash the chip:
avrdude: Device signature = 0x000000
avrdude: Yikes! Invalid device signature.
With a little searching, and in the tutorial #simplex linked to I've found, that I maybe need a crystal in my circuit, because the invalid device signature error could be caused by different clock frequencies. Or that's how I understood it.
Does that make sense?
And if I need a crystal, how do I connect it, when I'm using the ISP-header? I can't connect the crystal as in the tutorial you linked to #simplex, since I'm connecting to the ISP header