I recently completed the build of this sign display using OSH-Park PCBs (4-layer). I wrote the standard hello world application to check that the board functions. This was just to blink the status LED. That worked out fine, and so I went on to test that the CPU can drive the LED matrix, and that also is just fine, so the hardware is ok.
I now focus on the software. I do not like to use the Atmel ASF stuff because it brings in so much unnecessary stuff, so instead I write my own driver library and use gcc and CMSIS for the ARM CPU. The driver library is not too complex, it just sets up clocks and has high level GPIO functions. The only other important peripheral is the SPI interface. I have finished all the GPIO code, and am working on the clock/PLL setup code which is nearly done now. Then I'll be able to get the basic display multiplexing working.