Ok, thanks a lot guys!
I took the advice from CrossRoads and send now every 4th byte from Processing, which looks like this:
void loop(){
if (Serial.available() > 3) {
// shoot off feedback LED
digitalWrite(feedbackLED,HIGH);
// Register range from 0-3
// Pins range from 0-7
int arrivingByte = Serial.read();
Serial.println(arrivingByte);
int registerByte = 0; // will host the serial from processing
int pinByte = 0; // will host the serial from processing
// to do! find the right register+pin
sendToRegister(registerByte, pinByte);
// end and start again, so it doesn't get triggered by the serials used within the sendToRegister() function, which would start the Serial.available() again
Serial.end();
Serial.begin(9600);
}
digitalWrite(feedbackLED,LOW);
}