As I discussed privately with John and Kevin, I wondered why the 3-column layout. As they explained, the 3rd column is to hold the RST tool.
However, the header area (with journal title, menu items, and journal nav) as well as the footer do not need those 3 columns, so I changed our header and footer files to accomodate for what I believe is a nicer layout, the header and footer framing the page.
To accomplish this, I removed a <td></td> at the end of each specific row, in each file, and added a colspan="2" to the previous <td> which holds the header, nav, menu items and footer.
Another suggestion I would like to give is for the journal, especially in the administration area, to use 90% of the width of the page, or change the HTML code. The forms in the Edition and Submission tables, especially in portuguese and when many article images are included, break lines terribly.