Software Installation
You can now use the 16u2 as normal Arduino USB board like a Leonardo/Micro/Teensy with the Arduino IDE. Therefore you still need to get some software and install it properly. Arduino IDE 1.5.8 or higher is recommended.
You have to install new drivers since it will conflict with the official due to new USB functions it will use a different PID/VID). You can install the proper (unsigned) driver from the .inf file or as an alternative you can also install the (signed)Teensy drivers.
The driver file is named HoodLoader2.inf. Also see this tutorial on how to install the drivers (right click the .inf file and hit install). How to install drivers for Windows 8/8.1.
If you don't want to install the unsigned driver, you can also install the Teensy driver which works for every USB Serial device. It will then show up as Teensy USB-Serial and not as HoodLoader2 in the device manager. If you have both drivers installed it will show up as HoodLoader2. The Teensy driver recognizes any CDC USB device as Teensy USB Serial if no other driver is installed. This might be usefull if you plan to change the PID/VID for developing.
If you want it to be recognized as Uno/Mega edit the boards.txt definitions' VID and PID. I don't recommend this to a) know what Bootloader currently is on your board and b) it seems that with the official signed drivers wont work with unofficial HID modification.
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For your interest you can also use this (somehow outdated) older USB-Core with Lufa from Mattairtech.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.