The default templates are kept in the sc/templates/ directory for the store. If your store is the only one using the cgis you might have access to this directory but if you are sharing the cgis with other stores you will most likely not have access to that directory. Note that if you were to modify templates in this area they WILL be overwritten when the store/mall is upgraded so it is not a good idea to modify them.
User defined templates are kept in the data/templates/ directory. If you use the
Copy ShopSite template option on the Merchandising > Custom Template > ( Pages, Products, Shopping Cart, Includes, etc) screens to copy the templates that you need to modify they will be placed in your user defined templates area and won't be over written by an upgrade.
It may take a little work to find the exact files you need to copy and modify to get the look that you want.
If you go to
http://www.shopsite.com/templates/cookb ... ates.shtml
and find the template that you are modifying you can click on the link for More INfo on the theme and see a list of the template files used in that theme.
When you copy a template using the copy ShopSite template button you have to give it a different name from the ShopSite name. However once you have copied it you can then copy it again to have the same name as the ShopSite one and it will override the ShopSite template and use your changes.