I often find that the template manager is not very useful in terms of making modifications to a template. When you click "Save" in the template manager after editing the template HTML (index.php) or CSS (template_css.css) file, the manager takes you back to the list of installed templates. If you need to make another change, you have to re-open the Edit CSS or Edit HTML screen, which adds an extra step.
Another drawback of the template manager (in Joomla! 1.0.x) is that it only allows you to edit the "index.php" and "template_css.css" files. For some of the more advanced templates, there are more files that you may need to modify. You might also need to upload some more images for your modification.
That's where JoomlaXplorer comes in. It is a file manager that enables you to upload, modify, and delete files from your Joomla! installation via the administrator control panel. I use it every time I want to make a change to a template. For one thing, when I make a change to the HTML or CSS, it stays on the editor page. That way, I can check to see if the change I made produced the desired outcome or if I need to make more changes, and I can quickly go back and make more changes if necessary. It also allows me to edit any file in the template's folder and not just "index.php" and "template_css.css". Finally, it gives me the opportunity to replace images by uploading or deleting images based on my requirements.
So, if you haven't done so already, head over to the Joomla! Extensions Directory and get yourself a copy of JoomlaXplorer. It is the most useful component for web administrators available for Joomla!, and it will help you make changes to your site's template.