Software Installation
You can now use the 16u2 as normal Arduino USB board like a Leonardo/Micro/Teensy with the Arduino IDE. Therefore you need to get some software and install it properly. Arduino IDE 1.6 or higher is recommended.
You have to install new drivers since it will conflict with the official drivers due to new USB functions (it will use a different PID/VID).
The driver file is named HoodLoader2.inf. Right click the file and hit install. How to install unsigned drivers for Windows 8/8.1.
If you don't want to install the unsigned driver, as an alternative you can also install the Teensy driver which works for every USB Serial device. The Teensy driver recognizes any CDC USB device as Teensy USB-Serial (and not as HoodLoader2) if no other driver is installed. This might be useful if you plan to change the PID/VID for developing.
To get the 16u2 board definitions for uploading, copy this HoodLoader2 folder into your sketchbook like this: sketchbook/hardware/HoodLoader2/ Remove the '-master' postfix.
To actually use the USB functions you need a working USB-Core for the Arduino IDE. At the moment the Arduino IDE does not natively support the u2 series. Therefore you need to get the new USB-Core with the HID Project. The HID Project also adds new HID Devices to your USB-Core and some more improvements. (The HID Project can also be used for Arduino Leonardo/Micro and HoodLoader1.)
Go to the HID Project page to get the newest Arduino USB-Core for the 16u2. Follow the installation instructions carefully and try out the HoodLoader 2 related examples. If you update the HID Project files also ensure you have the newest HoodLoader2 board definition files.
For your interest you can also use this (somehow outdated) older USB-Core with Lufa from Mattairtech.
You should now have installed the bootloader itself, drivers, HL2 board definitions and HID Project. Read on how to use the bootloader and upload programs.