Some notes on your code:
- No need for your import, it is automatically done by Processing;
- Actually, I fail to see why you use an ArrayList there. This structure is good when you don't know in advance the total number of items, but here is it well defined from the start.
- Even more as you just change the value in place. Note that if you added the value from the start, you wouldn't need the test each time.
Here is a simplified version of your code:

1. int value;
2. int cols = 13;
3. int rows = 3;
4. int sizeX, sizeY;
5. boolean light;
6.  
7. int[] ledArray = new int[rows * cols];
8.  
9. void setup() {
10.   size(640, 480);
11.   background(255);
12.   smooth();
13.   sizeX = width / cols;
14.   sizeY = height / rows;
15.   println(sizeX);
16. }
17.  
18. void draw() {
19.   rect(0, 0, width, height);
20. }
21.  
22. void mousePressed() {
23.   if (mouseButton == LEFT) {
24.     value = 1;
25.     ledArray[0] = value;
26.     println("Light is on " + value);
27.     fill(255, 0, 0);
28.   }
29.   if (mouseButton == RIGHT) {
30.     value = 0;
31.     ledArray[0] = value;
32.     println("Light is off " + value);
33.     fill(0);
34.   }
35. }

Now, to manage each rectangle.
It isn't really hard.
First, I would simplify further your code:

1. int cols = 13;
2. int rows = 3;
3. int sizeX, sizeY;
4.  
5. int[] ledArray = new int[rows * cols];
6.  
7. void setup() {
8.   size(640, 480);
9.   background(255);
10.   smooth();
11.   sizeX = width / cols;
12.   sizeY = height / rows;
13.   println(sizeX);
14. }
15.  
16. void draw() {
17.   if (ledArray[0] == 1) {
18.     fill(255, 0, 0);
19.   } else {
20.     fill(0);
21.   }
22.   rect(0, 0, width, height);
23. }
24.  
25. void mousePressed() {
26.   if (mouseButton == LEFT) {
27.     ledArray[0] = 1;
28.   }
29.   if (mouseButton == RIGHT) {
30.     ledArray[0] = 0;
31.   }
32. }

(More to follow)
(Continuing)
Let's subdivide the display in the appropriate number of rectangles. We only need to change draw():

1. void draw() {
2.   background(255);
3.   for (int x = 0; x < cols; x++) {
4.     for (int y = 0; y < rows; y++) {
5.       int idx = y * cols + x;
6.       if (ledArray[idx] == 1) {
7.         fill(255, 0, 0);
8.       } else {
9.         fill(0);
10.       }
11.       rect(x * sizeX, y * sizeY, sizeX, sizeY);
12.     }
13.   }
14. }

Now, the hit test when pressing the mouse:

1. void mousePressed() {
2.   int x = mouseX / sizeX;
3.   int y = mouseY / sizeY;
4.   int idx = y * cols + x;
5.   if (mouseButton == LEFT) {
6.     ledArray[idx] = 1;
7.   }
8.   if (mouseButton == RIGHT) {
9.     ledArray[idx] = 0;
10.   }
11. }

Thank you benja and PhiLho you were most resourceful. What i was missing was the logic on how to divide the screen. I am still a beginner and learning. This should be a part of a communication between processing and arduino, more specifically and easy way to change the software for bigger boards and turn on or off led's. I would be using an SPI for this. I really don't know if this is the best approach, but i think it should work. Of course this is just at the starting point. benja that's why i was using the int values rather than bool. Nicely done with the border there :) and a nice clean code too. PhiLho that you for shortening my code i was using the java documentation for adding values. Thanks again, i am going back to coding.