Not all 100 pins of ATMega 2560 are used in arduino mega

RePuDiaToR:
how can i define (pinMode) does pins as digital input?
...
does i neet to define (pinMode) as output

If you're using MegaCore, you can just use those pins as you would any other Arduino pin. Note that the "MegaCore AVR Pinout" pin mapping does not match the Arduino Mega pin mapping: