In my projects, I used the Atxmega128A3U microcontroller by Atmel. To do so and easier, I built a board with all ports connected to the exterior with a flat cable and power included in the board as well as a crystall to operate at different frequencies. This board has helped me greatly, and I connect all projects through it. The next picture shows the different parts and how the connectors are attached. Each one can have different distributions and they are also shown. To program and debug I usually use the AVR, Jtagice3 as a PDI interface (1Mhz), but I have used as well and without problem the AVRISP mkII and the AVR Dragon. If you are interested in buying one of these at 10€ including connectors boards without soldering parts, you can contact me at my email linkntronix@gmail.com and I will send it to you. Ports and its pins' connections: Finally I show you the different parts of the connector,
How to program Atxmega128A3U by C language to control devices