See first comment for description. When plugged in, the board can be programmed directly with the DFU protocol. This can be done with Atmel tools, dfu-programmer or with a recent version of avrdude (using -c flip1). If you want another bootloader, for example Arduino, you'll have to flash it, be sure to actually force erase it twice and don't worry that it will not identify as an atmega32u4 to your programmer. After this the bootfuses etc. will be visible and you can program it as an arduino. Pick an 8Mhz/atmega32u4 board like the lilyUSB or Leonardo if using a 16Mhz crystal. You can also add a custom board to the Aruino boards.txt. For customizing the bootloader with a specific PID/Vid try this article: http://steven.casagrande.io/articles/compiling-arduino-caterina-with-new-vidpid/.

If you want to breadboard this first try this vertical breakout for the atmega32u4 with labels and fritzing file: https://workspace.circuitmaker.com/Projects/Details/Frido/tqfp44-breakout.