Purpleshades Template for Zencart V1.3
Re-read the authors comments in the download section on this template.
It is not a template that is targeted at the future and is what is called 'table based'. This is what Zen Cart was using in the pre 1.3.x releases. Beginning with 1.3.x Zen Cart is almost tableless and uses mostly css for styling.
There are several free templates that are based on the template default set of files and one of these will get you started in the correct direction.
As far as files that might get overwritten...the third forum in this section is about the override system and if you adhere to this for only those files that you edit, you will lose none of your customizations and have only a hand full of files that must be checked for changes.