Thank you for bothering to write.
I have the XMega A manual for the microcontroller and a schematic of the board.
CodeVision has a Wizard that writes a huge part of the code for me, all I have to do is configure the microcontroller using that wizard. (at least that's the step that I am having difficulties with)
Here is the microcontroller part of the schematic:

Here is an image on how the wizard looks like:

I'm having difficulties interpreting the schematic.