replace the header image with a custom banner

I would like to add a custom banner rotator to Atahualpa. A few versions back I knew how to do this, but things have changed and I'm stuck. Here is my code:
<?php echo do_shortcode("[all_in_one_bannerWithPlaylist settings_id='1']"); ?>
I read the posts on inserting a widget, but then I have to add another plugin, which I would rather not do. I would like to add that little piece of code to the appropriate php file, but cannot seem to find the proper place. I did get it to work, but it looks pretty crappy, so I know I didn't do it right - It's off center and will only ride above the menu. Please tell me how to edit the php correctly.