Both.
The header height is controlled by .
template.css (line 701)
#ja-header-inner
height:100px;
position:relative;
z-index:999;
And this Image.
template.css (line 689)
#ja-header
background:transparent url(../images/header-bg.png) no-repeat scroll left top;
line-height:normal;
So you need to edit height in the first bit of code to the height you require and the image (.. /images/header-bg.png) linked to in the second bit of code to the height you require
As for the background of the modules, there is quite a bit of css that needs adjusting as well as a couple of imaged from your templates images folder.
If you view your site with firefox and use the firebug plugin you can inspect any element of the module and it will point you towards the code or images that you need to change.