After starting up the Arduino IDE, first choose the board you have. Select 'Tools' -> 'Board' for this.
Choose the 'Linux GPIO / RasPi' programmer. That's under 'Tools' -> 'Programmer'.
When you're ready to upload your sketch to the board, make sure to use 'File' -> 'Upload Using Programmer'. The 'upload' button in the GUI only works on a AVRPi-32U4 with the Caterina bootloader running, and a USB cable connected.