5
Here's another way to look at it.
Themes control the "wrapper" for your site... the basic layout as it appears on every page. Templates control the presentation of information from modules.
If you are wanting to eliminate tables from your layout, I think you will spend most of your time with the theme.html file for the theme in question.
When you start looking at templates, you will find that most of those already use
for everything. (An exception might be a module that produces tabular data... a legitimate use for tables).
So the html files for the theme would be the ones to hit. These are found in the subdirectory for your theme. theme.html etc. As you move things from tables to div for layout, you will want to add an appropriate div class to your CSS file to style and position your layout div blocks.
(CSS defines styles for both themes and templates. Kind of a side issue. Most if not all of the colors, fonts, margins and widths, etc., should be controlled in the CSS, ideally. It is worth mentioning that when you download a theme created by someone it includes the CSS file, so the CSS is "part" of the theme... but, the styles in the file do impact the way template content looks.)
I hope that helps.