You can set those in your code, but remember to take into account there are different devices with different SPI pins. I feel it is best to call SPI.begin() and let it decide. Note the first three instructions.
SPIClass SPI;
void SPIClass::begin() {
// Set direction register for SCK and MOSI pin.
// MISO pin automatically overrides to INPUT.
// When the SS pin is set as OUTPUT, it can be used as
// a general purpose output port (it doesn't influence
// SPI operations).
pinMode(SCK, OUTPUT);
pinMode(MOSI, OUTPUT);
pinMode(SS, OUTPUT);
digitalWrite(SCK, LOW);
digitalWrite(MOSI, LOW);
digitalWrite(SS, HIGH);
// Warning: if the SS pin ever becomes a LOW INPUT then SPI
// automatically switches to Slave, so the data direction of
// the SS pin MUST be kept as OUTPUT.
SPCR |= _BV(MSTR);
SPCR |= _BV(SPE);
}