Atmel SAM E70 SPI Chip-Select (SPCS) lines

1. You use the DDRx register to define the direction of a pin (Data Direction Register). x is the name of the port you are using. Set the relevant bit to 1 for an output, and 0 for an input.

2. Does your mouse have Windows installed on it? No. The same with microcontrollers. They only need the code on them to perform their own task. Why would the slave need the software that runs on the master?

3. SPI is an incredibly simple protocol. The main thing to remember with it is it's full duplex and synchronous. If the slave needs to send data to the master then it is up to the master to request that data - the slave can't just send data at will to the master. Making sure the slave can respond to the SS signal fast enough is also important - you don't want to miss the first bit of the first byte coming in.

The SS line ( of this devices or others ) is completely ignored in the example since it is supposed to controlled by the software ( you have to do it ) as it states that in page 163 of that datasheet:

When configured as a Master, the SPI interface has no automatic control of the SS line. This must be handled by user software before communication can start. W hen this is do ne, writing a byte to the SPI Data Register starts the SPI clock generator, and the hardware shifts the 8 bits into the Slave.

I now this is about the other device SS but it implies that you should take care of this line on both sides ,So even in the sending part it is supposed to drive the SS of the slave low but it is not included

    void SPI_MasterTransmit(char cData)
{
    /* Start transmission */
    // set slave SS line to low is missing here
    SPDR = cData;

    /* Wait for transmission complete */
    while (!(SPSR & (1<<SPIF)));
}