I want to be clear, if you're going to do multi-touch you should really consider creating a custom controller. See below. This document is specifically about multi-touch support from the sample Gamepad controller

HFTInput

The HFTInput component supports the standard unity Input.touches see docs and Input.GetTouch function see docs.

In other words, like it's explained in "Your First HappyFunTimes Game you look up the HFTInput component in your Start function

private HFTInput m_hftInput;

// Use this for initialization
void Start () {
    m_hftInput = GetComponent<HFTInput>();
}

And then anywhere you'd use Input.something you instead use m_hftInput.something.

Note: HFTInput's touch functions return HFTInput.Touch objects, not Unity Touch objects.

Note: The Touch.rawPosition is currently in screen pixels of the Unity game not the controller.

The Unity Input API says those values are in pixels but they are assuming the game is running on the phone. In the case of HappyFunTimes each phone is different so having it be in phone screen pixels would make no sense unless you also knew the resolution of each phone. The controller could provide that info but that would make it more complicated for you.

Personally I'd prefer normalized values (0.0 to 1.0). If you want those then take Touch.rawPosition and divide x by Screen.width and y by Screen.height as in

HFTInput.Touch touch = m_hftInput.GetTouch(0);
float normalizedX = touch.x / Screen.width;
float normalziedY = touch.y / Screen.height;

HFTGamepad

The second way of getting multi-touch data is looking up buttons an axes on an HFTGamepad component.

Look up HFTGamepad component in your Start function.

private HFTGamepad m_gamepad;

// Use this for initialization
void Start () {
    m_gamepad = GetComponent<HFTGamepad>();
}

Then read the correct axes and buttons for each touch

void Update() {

   // check if first touch is pressed
   if (m_gamepad.button[HFTGamepad.BUTTON_TOUHCH0]) {
      // Get the normalized touch position (0 to 1)
      float x = m_gamepad.axes[HFTGamepad.AXIS_TOUCH0_X];  // range -1.0 to +1.0
      float y = m_gamepad.axes[HFTGamepad.AXIS_TOUCH0_Y];  // range -1.0 to +1.0
   }

   // check if second touch is pressed
   if (m_gamepad.button[HFTGamepad.BUTTON_TOUHCH1]) {
      // Get the normalized touch position (0 to 1)
      float x = m_gamepad.axes[HFTGamepad.AXIS_TOUCH1_X];  // range -1.0 to +1.0
      float y = m_gamepad.axes[HFTGamepad.AXIS_TOUCH1_Y];  // range -1.0 to +1.0
   }

   ...etc...

Up to ten touches are supported (limited of course by the phone and the browser's touch support)

    HFTGamepad.AXIS_TOUCH0_X
    HFTGamepad.AXIS_TOUCH0_Y
    HFTGamepad.AXIS_TOUCH1_X
    HFTGamepad.AXIS_TOUCH1_Y
    HFTGamepad.AXIS_TOUCH2_X
    HFTGamepad.AXIS_TOUCH2_Y
    HFTGamepad.AXIS_TOUCH3_X
    HFTGamepad.AXIS_TOUCH3_Y
    HFTGamepad.AXIS_TOUCH4_X
    HFTGamepad.AXIS_TOUCH4_Y
    HFTGamepad.AXIS_TOUCH5_X
    HFTGamepad.AXIS_TOUCH5_Y
    HFTGamepad.AXIS_TOUCH6_X
    HFTGamepad.AXIS_TOUCH6_Y
    HFTGamepad.AXIS_TOUCH7_X
    HFTGamepad.AXIS_TOUCH7_Y
    HFTGamepad.AXIS_TOUCH8_X
    HFTGamepad.AXIS_TOUCH8_Y
    HFTGamepad.AXIS_TOUCH9_X
    HFTGamepad.AXIS_TOUCH9_Y

    HFTGamepad.BUTTON_TOUCH0
    HFTGamepad.BUTTON_TOUCH1
    HFTGamepad.BUTTON_TOUCH2
    HFTGamepad.BUTTON_TOUCH3
    HFTGamepad.BUTTON_TOUCH4
    HFTGamepad.BUTTON_TOUCH5
    HFTGamepad.BUTTON_TOUCH6
    HFTGamepad.BUTTON_TOUCH7
    HFTGamepad.BUTTON_TOUCH8
    HFTGamepad.BUTTON_TOUCH9

You can see this in action by opening the ControllerTestScene in Assets/HappyFunTimes/Samples/Scenes included with the plugin. Run it. For each phone you connect you should see all of the buttons and axes.

To see the touch inputs select one of the connected phone's in the scene

And set the controller type to c_touch

Caution! Optimize your controller!

Multi-touch in the sample Gamepad controller is really just there for you to play with. For a 1-4 player game it might be fine but if you'd 40 players each sending 5 to 10 fingers of input every frame you're quickly going to run out of bandwidth

The truth is if you really want to do something fancy with touch controls you should create a custom controller. By that I mean you should edit or better copy Assets/WebPlayerTemplates/HappyFunTimes/controllers/gamepad/scripts/controller.js and Assets/WebPlayerTemplates/HappyFunTimes/controllers/gamepad/controller.html and process touch events in JavaScript on the phone. Figure out as much on the phone as you can and then only send the result to the game. For example lets say you wanted the phone to look like a slingshot. You should actually draw the band of the sling shot on the phone in JavaScript. Do touch processing on the phone to stretch the band to where the player is putting their finger and when they finally lift their finger just send the tension and direction to the game and maybe the orientation. That would keep communication between the game and the phone to a minimum and help ensure a good experience.