briefly and incompletely - you are going to have to go ahead and deal with the overrides issue and start using the correct templates. start by backing up your files...
to get familiar with what is talked about look in includes/templates/ you'll probably see classic and template_default listed. You need to have your template here ie. template_scrapbook.
Keep going a little deeper looking at includes/templates/template_default/ then you'll see a few more file folders etc common css images templates. read up on the Overrides threads. It won't make much sense at first but if you just go slow and try not to take shortcuts it will be easier. basically you are just going to copy over the template_default files to template_scrapbook. I'm not sure if you can just copy and rename it - maybe but research first. There may be some image files under classic you want and if you made some edits already you'll want to find and move those files to your new template_scrapbook directory. The system is going to automatically look for your template (template_scrapbook) before using classic and default.
If you make some changes and your website melts just revert to the copies you made.
after that has taken up some time (good investment - do now) ---
you have PHP files and CSS Stylesheet files
PHP files kind of tell the page what to do - talk to the database etc. The order in which you place command codes (like where you put the counter in the footer) determines in which order the text and images are going to show up on your webpage.
CSS stylesheet controls the look and placement of things - text color, left or right aligned, colors etc.
so the PHP tpl_blahblah.php files in the templates directory control the basic functions and look of the site, and the CSS fine tunes things - that's not totally correct but it serves our purposes...there can be more than one css stylesheet used on your site depending on what you are trying to do.( different contributions etc) and if you used the 'classic' you have two stylesheets by default - which if you do some searches on the forum will show you that you're starting out on the wrong foot and should maybe use the template_default stylesheet or one of the contributed free templates available in downloads.
**for fun **you could download a template - put it in the templates directory and WHAM you'll see a completely different site appear. move it out if you don't want it, or you could edit the CSS stylesheet for different colors etc.
if you had the firefox web developer tool kit installed you could open your page, click
CSS - view CSS and it would show you the exact file locations
whew, I didn't realize I knew so much and only enough to cause havoc...