How I can divide information stream from bluetooth hc-06?
Your code have various issues.

This:

   if(color==1)
      {
       chosed_color = rPin;
      digitalWrite( rPin, HIGH );       
      digitalWrite(rPin, LOW);  
       return chosed_color;
      }


means that when you find a color, you exit loop() instead of reading the val variable.

Serial.read

Serial.read read only one byte. If you need to read an arbitrary integer, need Serial.parseInt or some elaborate solution. As it, you are only able to read one-digit integer values.

Worse, when you type "1" in the Serial Monitor, what the program received is the value 49 (the ascii code for char 1).

Also, you have to filter non interesting chars, like LF, CR, commas or whatever char you use as delimitir.

Please, read the excelent post by Majenko about Reading Serial on the Arduino.

Here a better version of your code. It is very basic and lacks all error checking, etc.

const int rPin = 3;
const int gPin = 5;
const int bPin = 6;
int pins[3] = {rPin, gPin, bPin};

void setup()
{
    Serial.begin(9600);
    pinMode(rPin, OUTPUT);
    pinMode(gPin, OUTPUT);
    pinMode(bPin, OUTPUT);
}

void loop()
{
    if(Serial.available()&gt;0) {
        int color = Serial.read();
        int chosed_color = pins[color-1];
        digitalWrite(chosed_color, HIGH);
        digitalWrite(chosed_color, LOW);

        if(Serial.available()&gt;0) {
            int val = Serial.read();
            digitalWrite(chosed_color, HIGH); // I suppose you want this
            delay(val);
            digitalWrite(chosed_color, LOW);
            delay(val);
        }
    }
}