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The approach noted in the question – having an identifying character at the front of each number – is a workable approach. Other approaches include:
• always sending numbers in pairs, eg 2000,300 would denote A2000 B300.
• encoding the A or B as part of the number; eg, the range 0-4999 could denote A delays of 0 to 4999, while the range 5000-9999 could denote B delays of 0 to 4999.
• sending A delays via decimal digits, and B delays via letter-substitutes for digits; eg DAA could encode a B delay of 300.

One of the easiest-to-parse approaches is to have an identifying character at the end of each number, rather than at the front. This allows your code to pick up digits until a letter appears, and then dispatch based on the letter. Here's some example code:

// Sketch that accepts numbers and action code via serial input.
// Silently ignores any numbers not followed by a valid action letter.
// Does not test for number overflow.      - jiw 3 Nov 2016

void setup() {
  Serial.begin(115200);         // init serial port
}

unsigned int val=0;
void loop() {
  char inc;
  while (Serial.available()) { // Get characters
    inc = Serial.read();
    if (inc >= '0' && inc <= '9') {
      val = 10*val + (inc-'0');
    } else {
      switch (toupper(inc)) {
      case 'A':
        Serial.print("Case A got ");
        Serial.println(val);
        break;
      case 'B':
        Serial.print("Case B got ");
        Serial.println(val);
        break;
      default :
        ; // handle blanks, returns, etc
      }
      val = 0;  // Set val to zero after any non-digit
    }
  }
}