I tried to make the header fixed as described on this thread. It worked well except for a page witha form from contact form 7. When that page scrolled up the input boxes showed over the header.
I undid it for now, but can easily redo if you would like to see what I mean.

Related thread here.

What version of Atahualpa and WP?
What is the URL?

WP 3.3.1
Atahualpa 3.7.3
http://lowerwatt.com/getquote/

I will redo this so that you can see.

I have put it back to the skewed way mentioned above for your viewing

Try increasing the z-index for #header-wrap

As a learner in CSS and wordpress as a whole I am not really sure how to do this or what z-index is. As per Juggledad in this thread I added the following code to CSS inserts:

div.header-image-container {z-index: 10;}

This took care of the form showing through the images and the menu items. It still shows through the menu bar where there are no items.

Maybe I should have made them one thread.

I think I have it figured out between the two of you. I added this:

#header-wrap {z-index: 10;}

It took care of all things showing through the entire header. Now I just need to get the sidebars straightened out as described here.