First of all it is "Javascript" not "Java Scripts".

Second, the differences go far beyond how the machine handles execution of the code.  Java is a strongly typed language following the classical inheritance model.  Javascript is a weakly typed language, and uses the prototype inheritance model. 

Java was created by Sun Microsystems as a "write once, run anywhere" language, and it achieves that goal by running inside a JVM - Java Virtual Machine.  It is indeed a compiled language, as you cannot run Java from source, but the argument can be made that it is also an interpreted language, as the compiled source - bytecode - is not run natively, but rather interpreted by the JVM.

Javascript was originally developed by Brenden Eich at Netscape, as a browser-based, client-side language.  It was first called "LiveScript", and I've heard many theories on why the name was changed.  The language, however, has little in common with Java.

The differences between compiled and interpreted code will be lost on most entry-level programmers.  The best advice is simply to ignore Java until you have a grasp of Javascript, and know the difference between client-side and server-side.  Java may be used as a server-side language, alone or in combination with JSP - this is perfectly acceptable, and is often done in corporate environments, but most independent developers use PHP or other open-source language (Python, Perl, Ruby, etc.)

There are, of course, ways to embed Java into a webpage.  The number of users without Java support far outnumber those without javascript support, though.  I can't think of a reason to write a modern application with client-side Java.