"I did end up using the blank sidebox contribution in the end. I had a slight problem with it... I tried to duplicate it, renaming the 3 files and the code in them. I wanted 2 pemanent adds in both rifgt and left columns. I managed to display 2 different headers for each sidebox but the images were the same, even though I had different image links in each "blank_sidebox_defines.php" and "blank_sidebox_defines2.php" file."
For your duplicated blank sidebox check the content of the /includes/modules/sideboxes/blank_sidebox2.php file to make sure it has the line
require($template->get_template_dir('tpl_blank_sidebox2.php',DIR_WS_TEMPLATE, $current_page_base,'sideboxes'). '/tpl_blank_sidebox2.php');
It may be that your duplicated sidebox is using the first sidebox template for it's content.
If that doesn't solve the problem have a close second look through the files to make sure you updated all of the filenames and variables correctly.
"What I would like to do ultimately, is have the 2 banner side boxes display the same banners at all times. I will need to know how to do this once we have adds that link externally. We will need the stats you get with the banners when this happens."
Do you mean have the two banner sideboxes display the same banner as each other (with perhaps multiple banners images in the rotation)? So both banners would have, say, four banners that could be displayed, but they always display the same one as each other. If so then you could come up with code in the template file for each banner that saved some global variable when the sidebox is displayed. If the variable hasn't been set then the first sidebox would randomly select a banner to display and then declare a variable with the value of the chosen banner. The second time the banner sidebox is displayed it will find that the variable has been declared, and will then display the same banner as the first banner sidebox.