Help with script manager and Java Script

On my aspx page I am using a web service to feed html to drop-down style menus which display links to a user's info (these are hidden divs controlled by javascript). There is a js file which contains the js functions that display and hide the menu divs and then there are also other functions for the webservice which are embedded directly in the page's header. I want to somehow put the embedded javascript functions that pertain to the websevice on the js file intead of the page's header.  Bellow is the code for the aspx page that contains the javascript....
<%@ Master Language="C#" AutoEventWireup="true" CodeFile="MasterPage.master.cs" Inherits="MasterPage" %> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/x ...