Registers involved:

GPIO:
DDRA: Data Direction Register for Port A= 0xFF for output (Port A- pin 22:29)
DDRB: Data Direction Register for Port B= 0x00 for input (Port B- pin 53:50[B0:B3] & pin 10:13[B4:B7] ) 
DDRC: Data Direction Register for Port C= 0xFF for output (Port C- pin 37:30)

PORTB: Port B Data Register
PINB: Port B Input Pins Address

About pull-up and pull-down resistors: