I'm very sorry if this an been answered before but I have looked every where can cant find a solution.

I am using a background image as a header also on my website, its on a Atahualpa 3.4.9. I wanted to put a separate image over the background using java that people can click on.
I was also wondering if I could make certain parts of the background image linkable?

The website is http://lakewooditsupport.co.uk

The code is as follows.

'<a id="islpronto_link" href="mailto:info@lakewooditsupport.co.uk"><img id="islpronto_image" alt="Live chat" src="http://www.lakewooditsupport.co.uk/wp-content/themes/atahualpa/images/islpronto/islpronto-chat.jpg" style="border:none"/></a>
<script type="text/javascript" src="http://islpronto.islonline.net/live/islpronto/public/chat.js?d=lakewooditsupport"></script>'

I have managed to create an image map using java on my home page but I still cant get the background image to link.

You could try putting a link in your HTML and position it where you want (use a border when you position it so you can see it) then give it a high z-index, though the java may ignore it...