I'm assuming you're using Javascript.

Everything in one file is in one class. private variables and functions can only be used inside that class. public variables and functions can be used by that class and anything that references that class.

All of your scripts are a subtype of Component. So like how you can do var myRigidbody = GetComponent( "Rigidbody"), you can do the same thing with your classes.

Once you have a reference to your custom component type, you can then call functions and access variables just like anything else.

As a basic example:

MyClass.js:

var counter : int = 0;

function DoIncrementCounter()
{
   counter += 1;
   WillNotBeAbleToCallThisExternally();
}

private function WillNotBeAbleToCallThisExternally()
{
     Debug.Log( "private function" );
}

Notice there's no public declaration since in Javascript everything is assumed to be public by default. In C# it's the opposite, where everything is assumed to be private.

In another script that's attached to the same game object as the above is, you can do this:

var myClass = GetComponent( "MyClass" );
var myClassCounter = myClass.counter;
myClass.DoIncrementCounter();

And that should be obvious what that does. However you won't be able to call the private function, or access private variables with a reference to your class.

If that script is on another game object, first you have to get a reference to the game object that your script is on. From there it's the same, you would just call GetComponent on the game object reference itself. You can search by name (bad idea, but what most people start with since it makes the most obvious sense), or you can set up references inside your script and set things up ahead of time in the scene or via instantiation.