Your issue here is that there is nothing in your code that checks if you are picking up the game objects and increasing your score. Here is a way to fix that:

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Step Zero: Notes

I need to sleep right now, and as such I won't be able to proofread this answer. There could be spelling mistakes, which you need to be mindful of, ESPECIALLY if they are in code

I use C# more than Javascript, so if there is any syntax wrong, please point it out :)

If there are still any errors/issues, please tell EXACTLY what is going wrong, AS WELL AS any errors that come from the unity engine

Step One: Editor

Add two game object cubes, one named DepositArea and one named ScoreBlock. Put them a fair distance apart. Set the tag for the DepositArea to be Deposit, while the tag for the score block to be ScoreBlock.

Check online if you are not sure how to tag objects

Then, set both of their colliders to be OnTrigger. Again, check if the internet if unsure how.

Step One.Five: Setting up some variables

In the beginning of the script, we assigned some variables, but never gave them a value. It would be best if we did. This is to just remove any possible errors

 //This is how many you are carrying. In beginning, you are carrying none, so set this to 0
 var carrying : int = 0;
 // This is how many you can carry at one time. Set this to what you like (here, 10)
 var carryLimit : int = 10;
 //This is how many you have deposited.In beginning, you have deposited none, so set this to 0
 var deposited : int = 0;
 // This is how many you need to win. Set this to what you like (here, 5)
 var winScore : int = 5;

Step Two: Increase Carrying Score by Code

Now we need to actually track the amount of blocks you are carrying. Put a new function inside the script, and set it to public:

 public function OnTriggerEnter (objectCollided: Collider) 
     {
         // Something;
     }

This function will execute everytime you hit an object that is marked OnTrigger. Now, check if that object has the tag ScoreBlock, so we know we are hitting a Score Block

 public function OnTriggerEnter (objectCollided: Collider) 
     {
         if (objectCollided.transform.tag == "ScoreBlock")
             {
                  // Something;
             }
     }

Now, we are checking if the object we are collided is a Score Block, by checking if it has the tag Score Block. If it does, let us increase how many you are carrying.

 public function OnTriggerEnter (objectCollided: Collider) 
     {
         if (objectCollided.transform.tag == "ScoreBlock")
             {
                  carrying++;
             }
     }

This will simply take how many you are carrying (In this case, 0) and add a 1 to it. Now, lets work on the Deposit Area!

Step Three: Increase Score when deposited by Code

Now, what we want to do is to do the exact same thing as before, but instead of looking if we hit a ScoreBlock, lets check if we are hitting a DepositBlock. We do both in an if statement inside the function OnTriggerEnter

 public function OnTriggerEnter (objectCollided: Collider) 
     {
         if (objectCollided.transform.tag == "ScoreBlock")
             {
                  carrying++;
             }
         if (objectCollided.transform.tag == "Deposit")
             {
                  // Something;
             }
     }

Now, instead of increasing the carrying number, lets increase how many we have deposited by how many carrying we have

 public function OnTriggerEnter (objectCollided: Collider) 
     {
         if (objectCollided.transform.tag == "ScoreBlock")
             {
                  carrying++;
             }
         if (objectCollided.transform.tag == "Deposit")
             {
                  deposited += carrying;
             }
     }

What did does is increase deposited by our current carrying score. It is the same thing as writing deposited = deposited + carrying, its just more concise. Now, we also need to reset the carrying score, so we can't just cheat and keep tapping the Deposit area with how much we previously carried

 public function OnTriggerEnter (objectCollided: Collider) 
     {
         if (objectCollided.transform.tag == "ScoreBlock")
             {
                  carrying++;
             }
         if (objectCollided.transform.tag == "Deposit")
             {
                  deposited += carrying;
                  carrying = 0;
             }
     }

Step Four: Done!

That is all we should need to do. Everytime you hit an object with the tag ScoreBlock, it will increase carrying by one. Whenever you hit the Deposit object, it will increase the deposit score with ScoreBlock, AS well as reset it to 0.

If there are any more problems, just say so :)

Step Five: Edited Code

MAKE SURE TO READ THE TEXT BEFOREHAND, INCREDIBLY IMPORTANT

 var carrying : int; = 0
 var carryLimit : int; = 10
 var deposited : int; = 0
 var winScore : int; = 5                            // How many orbs must be deposited to win
  
 var gameLength : int;                            // Length in seconds
  
 var guiMessage : GameObject;                    // Prefab for one-shot messages
  
  
 // GUIText objects that must be assigned in editor
 var carryingGui : GUIText;                        
 var depositedGui : GUIText;
 var timerGui : GUIText;
  
  
 // Sound fx and voices for different events
 var collectSounds : AudioClip[];
 var winSound : AudioClip;
 var loseSound : AudioClip;
 var pickupSound : AudioClip;
 var depositSound : AudioClip;
  
 private var timeSinceLastPlay : float;            // Last time we played a voice for pickup
 private var timeLeft : float;
  
 public function Start()
 {
     timeLeft = gameLength;
     timeSinceLastPlay = Time.time;
     UpdateCarryingGui();
     UpdateDepositedGui();
     CheckTime();
 }
  
 function UpdateCarryingGui()
 {
      carryingGui.text = "   X " + carrying + " of " + carryLimit;    
 }
 
 function UpdateDepositedGui()
 {
      depositedGui.text = " : " + deposited + " of " + winScore;    
 }
 
 function UpdateTimerGui()
 {
     timerGui.text = "   " + TimeRemaining();        
 }
 
 private function CheckTime()
 {
     // Rather than using Update(), use a co-routine that controls the timer.
     // We only need to check the timer once every second, not multiple times
     // per second.
     while ( timeLeft > 0 )
     {
         UpdateTimerGui();        
         yield WaitForSeconds(1);
         timeLeft -= 1;
     }
     UpdateTimerGui();
     EndGame();
 }    
 
 // This is a utility function to a play one shot audio at a specific position
 // and at a specific volume
 function PlayAudioClip( clip : AudioClip, position : Vector3, volume : float )
 {
     var go = new GameObject( "One shot audio" );
     go.transform.position = position;
     var source : AudioSource = go.AddComponent( AudioSource );
     source.rolloffMode = AudioRolloffMode.Logarithmic;
     source.clip = clip;
     source.volume = volume;
     source.Play();
     Destroy( go, clip.length );
     return source;
 }
 
 private function EndGame()
 {
     var animationController : AnimationController = GetComponent( AnimationController );
     var prefab : GameObject = Instantiate(guiMessage);
     var endMessage : GUIText = prefab.GetComponent( GUIText );
     
 
     if(deposited >= winScore)
     {
         //Player wins
         timeleft=0;
         endMessage.text = "You win!";
         PlayAudioClip( winSound, Vector3.zero, 1.0 );
         animationController.animationTarget.Play( "WIN" );
     }
     else
     {
         //Player loses
         endMessage.text = "Ran out of time!";
         PlayAudioClip( loseSound, Vector3.zero, 1.0 );        
         animationController.animationTarget.Play( "LOSE" );        
     }
     
     // Alert other components on this GameObject that the game has ended
     SendMessage( "OnEndGame" );
     
     while( true )
     {
         // Wait for a touch before reloading the intro level
         yield WaitForFixedUpdate();
         if ( Input.touchCount > 0 && Input.GetTouch( 0 ).phase == TouchPhase.Began )
             break;
     }
     
     Application.LoadLevel( 0 );
 }
 
 public function Pickup( pickup : ParticlePickup )
 {
     if ( carrying < carryLimit )
     {
         carrying++;
         UpdateCarryingGui();         
         
         // We don't want a voice played for every pickup as this would be annoying.
         // Only allow a voice to play with a random percentage of chance and only
         // after a minimum time has passed.
         var minTimeBetweenPlays = 5;
         if ( Random.value < 0.1 && Time.time > ( minTimeBetweenPlays + timeSinceLastPlay ) )
         {
             PlayAudioClip( collectSounds[ Random.Range( 0, collectSounds.length ) ], Vector3.zero, 0.25 );
             timeSinceLastPlay = Time.time;
          }
          
         pickup.Collected();    
         PlayAudioClip( pickupSound, pickup.transform.position, 1.0 );
     }
     else
     {
         var warning : GameObject = Instantiate( guiMessage );
         warning.guiText.text = "You can't carry any more";
         Destroy(warning, 2);
     }
     
     // Show the player where to deposit the orbs
      if ( carrying >= carryLimit )
         pickup.emitter.SendMessage( "ActivateDepository" );         
 }
 
 public function Deposit()
 {
     deposited += carrying;
     carrying = 0;
     UpdateCarryingGui();
     UpdateDepositedGui();
     PlayAudioClip( depositSound, transform.position, 1.0 );     
  }
  
 public function TimeRemaining() : String
 {
     var remaining : int = timeLeft;
     var val : String;
     if(remaining > 59) // Insert # of minutes
      val+= remaining / 60 + ".";
     
     if(remaining >= 0) // Add # of seconds
     {
         var seconds : String = (remaining % 60).ToString();
         if(seconds.length  < 2)
             val += "0" + seconds; // insert leading 0
         else
             val += seconds;
     }
         
     return val;
 }

 public function OnTriggerEnter (objectCollided: Collider) 
     {
         if (objectCollided.transform.tag == "ScoreBlock")
             {
                  carrying++;
             }
         if (objectCollided.transform.tag == "Deposit")
             {
                  deposited += carrying;
                  carrying = 0;
             }
     }

 if(deposited >= winScore && timeLeft >= 0)
     {
         //Player wins
         timeLeft=0;