I want to use ATmega2560 MC, but it manufactured only as surface mount IC which means i must make PCB to use it. I searched for a per-made kit and found Arduino Mega R3 board contains the desired MC. (It contains less I/O pins but that's OK for now). Can i implement my code (without any arduino code) in this board? or should i modify it to work with Arduino, also if it runs in the board will it be the same as normal IC or there will be differences in speed.
The MCU in the Arduino Mega2560 is a stock ATmega2560. There is no need to use the Arduino libraries to program it and no need to use the Arduino tools to communicate with it; avr-gcc and avrdude will work with it as normal. Note that you will need to select the appropriate programmer/protocol in avrdude for the bootloader programmed on the chip if you want to program it via serial rather than ISP.