Atmega 2560 pd6 control possible?

From the datasheet

The below program will show you the configuration for timer/counter1

void setup()
{
  Serial.begin(115200);
#if defined TCCR1B
  Serial.println("TCCR1B exists");
  if (TCCR1B < 0x10)
    Serial.print("0");
  Serial.println(TCCR1B, HEX);
  Serial.println("Clock select bits (CS12..10)");
  Serial.print((TCCR1B & 0x04) == 0x04);
  Serial.print((TCCR1B & 0x02) == 0x02);
  Serial.println((TCCR1B & 0x01) == 0x01);
#else
  Serial.println("TCCR1B does not exist");
#endif
}

void loop()
{
  // put your main code here, to run repeatedly:
}

It will show the clock select bits as set by the Arduino core; match it with the table in the second screenshot above.