Ok I got it, its actually pretty simple. I will demonstrate it using my website for you.
Make a blank html file and copy this code into it. Then run it in the browser.
Code:
<html>
<head>
<script language="javascript" type="text/javascript">
<!--
/****************************************************
Author: Eric King
Url: http://redrival.com/eak/index.shtml
This script is free to use as long as this info is left in
Featured on Dynamic Drive script library (http://www.dynamicdrive.com)
****************************************************/
var win=null;
function NewWindow(mypage,myname,w,h,scroll,pos){
if(pos=="random"){LeftPosition=(screen.width)?Math.floor(Math.random()*(screen.width-w)):100;TopPosition=(screen.height)?Math.floor(Math.random()*((screen.height-h)-75)):100;}
if(pos=="center"){LeftPosition=(screen.width)?(screen.width-w)/2:100;TopPosition=(screen.height)?(screen.height-h)/2:100;}
else if((pos!="center" && pos!="random") || pos==null){LeftPosition=0;TopPosition=20}
settings='width='+w+',height='+h+',top='+TopPosition+',left='+LeftPosition+',scrollbars='+scroll+',location=no,directories=no,status=no,menubar=no,toolbar=no,resizable=no';
win=window.open(mypage,myname,settings);}
// -->
</script>
</head>
<body>
<a href="http://www.jmcanineservices.com/training.php#puppy" onclick="NewWindow(this.href,'mywin','500','600','no','center');return false" onfocus="this.blur()">YourLinkText</a>
</body>
</html>
Now if you notice that when you open the window it jumps automatically to the puppy section of the website I built. This is achieved by adding a div tag with an id name surrounding the info i want to jump to. So by doing this youll notice that I added into the URL of the link the #puppy part. This tells it to automatically to go to that div on the page.
Code:
<a href="http://www.jmcanineservices.com/training.php#puppy"
<!-- You will see that I added this div tag id into the URL-->
Code:
<div id="puppy">Content goes here that you want to jump too</div>
Hope that is what you were looking for 
Here is the page on the site i sent you too so you can see how far down it takes you
http://www.jmcanineservices.com/training.php
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