The Atmel Studio project can be found in the Studio Project folder in the zip-file accompanying this application note, and is called WINC_mega. By changing the device in the Device tab of the project properties (Alt+F7), it can be recompiled for any megaAVR Xplained Mini board.
The megaAVR communicates with the ATWINC1500 module via SPI and uses Timer/Counter1 to time when to send UDP packets.
The Xplained Mini board can be programmed and debugged with the onboard embedded debugger and Atmel Studio. The WINC_mega_328p.hex file found in the Studio Project\programmable folder has been compiled for the ATmega328 and can be programmed directly via ISP if you are using an ATmega328 device.