Apologies for that missing tutorial. I shall really invest some time into writing it finally.
I've answered this question on the mailing list last year: https://groups.google.com/d/msg/paperjs/C6F0XFlplqM/_67AMqCR_nAJ
Scoped PaperScript run inside the global scope, and have access to all elements of the global scope. The normal JavaScripts running in the global scope (= window) will not see these PaperScopes, and won't have access to their variables.
There is a simple solution to exchange information between the two: Simply declare a global structure that you use to exchange tings back and forth, e.g.
window.globals = {
someValue: 10,
someFunction: function() { alert(globals.someValue); }
};
In your PaperScript, you can then access this simply through 'globals', since it's in the window scope:
globals.someValue = 20;
globals.someFunction();
And in the same way, you can use this structure from normal JavaScript.