The templates_c directory is created by smarty when it compiles your templates.

If you delete this directory in total it will recreate it next time a page is called.

As far as design changes in home.php .. the PHP only control the functions and which template files (which control the look) are used. Any changes to the look and feel should be made in the .tpl files, whereas underlying code changes in the way that x-cart operates should be done in the php files.