I need to program a bare Atmega2560 chip that'll be on a custom made PCB. I would like to use an Arduino UNO or Arduino Mega2560 to act as the ISP. I've looked at the link provided by Arduino on how to burn the bootloader to the bare chip by connecting the 6 pins: MISO,MOSI, SS, SCK, 5 V, and GND. http://arduino.cc/en/Tutorial/ArduinoToBreadboard
After this, you remove the MCU from the Arduino and wire RX and TX to some pins to the Atmega 2560. What I am confused about is what pins do I need to map to from the Arduino to my Atmega 2560 in order to upload sketches using the Arduino IDE. Also what capacitors and resistors would be needed as well.