Should be a piece of cake because you are using a mega board which has four hardware uarts. You could continue to use
Serial.xxxx() functions to upload your sketches and send debug messages to the arduino IDE serial monitor as you develop your sketch. Then use Serialx.yyy() functions where x = 1,2,or 3 to 'talk' to your external controlller. Just wire the proper Tx pin number corresponding to the serialx channel you use to your external controller along with +5 and ground wires. Here is reference page for uart communications.