Ordinary Arduinos have a USB-UART chip and talk to the AVR by serial.
Here USB goes to the 32U4 and you can only talk to the bootloader (which pretends to be a USB-UART chip, if you use the Leonardo one).
Once your firmware is running, the functionality is gone. You would need to link some USB library into your code and implement your own USB debug.
It looks like what you have done is set up the MCU's built-in UART. That's an option too, but you now need to connect some external USB-UART dongle to the TX/RX pins, because your board doesn't have that. Mind voltage levels - the dongles come in either 3.3V or 5V, some of them may work with both.