Templates are found in the templates/ directory.
You select one in "Sitewide Settings".
The customized template sets are an option, if someone has particular layout needs.
The theme (.css) should be enough to suit most people's needs. In case
you need a rather exotic layout, say you don't need certain
information or you want the layout to be readable on a handheld device
over a slow network link, you can create your own template set. Simply
copy the whole templates/phpaga/ directory to a
new name, say templates/mytheme/, and edit the
files at will. You can, for example, leave out all the graphs and
optimize the layout for 200x160 pixel screens.
In general, it is not recommended that users create their own template set unless they really want to keep up with development. Whenever we introduce a new variable (or remove an existing one) in one of the template files, this change would need to be applied to the customized template set too. If you do venture into this area, be sure to contact us here at phpaga, and contribute those changes for everyone to benefit from. That's what open source is all about after all.