How can I split my javascript code into separate files?

You should have one global namespacing object which every module has to access and write to. Modify your files like so:

// employe.js

window.myNameSpace = window.myNameSpace || { };

myNameSpace.Employee = function() {
    this.name = "";
    this.dept = "general";
};

and Manager.js could look like

// Manager.js

window.myNameSpace = window.myNameSpace || { };

myNameSpace.Manager = function() {
    this.reports = [];
}
myNameSpace.Manager.prototype = new myNameSpace.Employee;

This is of course a very simplified example. Because the order of loading files and dependencies is not child-play. There are some good librarys and patterns available, I recommend you looking at requireJS and AMD or CommonJS module patterns. http://requirejs.org/

You don't need to do anything differently. Just include the script files and they work as if it was a single file.

Javascript doesn't have file scope. Once the code is parsed it doesn't matter where the code came from.