Bandofcs:
What about crystals and such? I only see a 32khz and 12Mhz oscillator. Where is the 90Mhz 1?I am intending to use the acr isp mkii to program the microcontroller. As such i would like to know all necessary connections i have to connect in order for that to work.
Based on given schematic, i figured i have to at least connect the crystals, the vdd, the gnds, miso, sck, mosi, master reset etc.
Did i miss anything important?
Well, if you want the bare minimum, to just flash an LED, you can use the internal RC oscillator. If you don't want to go fiddling with startup code, then you better fit the 12MHz crystal. the 32kHz crystal is used for the real time clock, you can decide whether you need that or not.
AVR specific tools will not work with Atmel SAM series, they are completely different architecture. If you just want to program the chip, you can use the builtin bootloader and the SAM-BA programming software from Atmel.