Measuring the capacitance of 2 capacitors at a time
Before we get started, there are a few problems with your code.

First, I wouldn't check for ==648 or ==0: what if you miss it by a moment and it jumps to 649, or it doesn't quite discharge to 0v?  I'd use &gt;=648 and &lt;=2 (or some other similarly low number - experimentation required).

How is your circuit connected?  I can't quite get my head around the charge and discharge pins, but I'll stick with what you have, assuming it works.

You say you want measurements every 30s, but don't say how long they take. (I have no idea of the capacitance of your bottle.)  My code assumes it takes much less than 30s to measure one bottle.  If it takes near to 30s to do one, this won't work.

I'll also assume your code works.  This is a bad assumption, since it won't even compile (capital I in if) but regardless, that's what I'll assume.

All that being said, here's the code:

// Pins connections
int analogPinA = 0;
int analogPinB = 1;
int chargePinA = 13;
int chargePinB = 12;
int dischargePinA = 11;
int dischargePinB = 10;

// Resistor being used
int resistorValue = 10000;

void setup()
{
  pinMode(chargePinA, OUTPUT);
  pinMode(chargePinB, OUTPUT);
  digitalWrite(chargePinA, LOW);
  digitalWrite(chargePinB, LOW);
  pinMode(dischargePinA, OUTPUT);
  pinMode(dischargePinB, OUTPUT);
  digitalWrite(dischargePinA, LOW);
  digitalWrite(dischargePinB, LOW);
  Serial.begin(9600);
}

// Measure the capacitance of specified capacitor
float measureCapacitance(int analogPin, int chargePin, int dischargePin)
{
    // Ensure the capacitor is discharged
    digitalWrite(dischargePin, LOW);
    while (analogRead(analogPin)&gt;2) { /* Do nothing */ }
    pinMode(dischargePin, INPUT);

    // Start charging
    unsigned long startTime = millis();
    digitalWrite(chargePin, HIGH);

    // Wait for the capacitor to charge
    while (analogRead(analogPin)&lt;=648) { /* Do nothing */ }
    unsigned long endTime = millis();

    // Start it discharging again, ready for next time
    pinMode(dischargePin, OUTPUT);
    digitalWrite(dischargePin, LOW);

    // Calculate measured capacitance 
    unsigned long elapsedTime = endTime - startTime;
    float microFarads = ((float)elapsedTime / resistorValue) * 1000;
    return microFarads;
}

void loop()
{
    // Measure capacitance of first bottle
    float microFarads = measureCapacitance(analogPinA, chargePinA, dischargePinA);
    if (microFarads &lt;= X) // X is an arbitrary capacitance when the bottle is empty
    {
      Serial.println("Bottle A is empty");
    }

    // Measure capacitance of second bottle
    float microFarads = measureCapacitance(analogPinB, chargePinB, dischargePinB);
    if (microFarads &lt;= X) // X is an arbitrary capacitance when the bottle is empty
    {
      Serial.println("Bottle B is empty");
    }
}