Ok, figured it out on my own again. Here is the solution for others that need it. First change the body background to what color you want in the margins. Then I added a div container around everything by going to default.php under pages in the jat3 folder and inserting it directly inside the body tags. You might be able to just edit the ja-wrapper to do this, but I decided to just insert a new div. I added the following properties to the css for this new div:
background-color: #FFFFFF;
margin: 0 auto;
padding: 0 10px;
position: relative;
width: 980px;
and changed main-inner1 to #fff or whatever inside color you want. This is for the space between modules in the main content area, while the new div covers header and other parts. Gotta love joomlart templates, easily modifiable.