setTemplateRepository(string_or_array)Specifies where to look for templates. If given a string, it adds it to the list of paths searched. If given array, it replaces the list.
This doesn't mean all your files need to be in the root directory, you can use sub folders to organize your template designer's work. It's just a shortcut which will allow you to reference templates without specifying the real path, but instead their relative path within the repository.
It's like include_path, but for PHPTAL templates only.
setPhpCodeDestination(path)To tell PHPTAL where to store its intermediate (temporary) PHP files. By default it uses directory given by PHP's sys_get_tmp_dir(), which usually is '/tmp/' directory.
setPhpCodeExtension(string)What filename extension should be used for intermediate PHP files. The default is php and frankly, there's no reason to change it.
setCacheLifetime(num_days)Maximum number of days intermediate files and fragments cached with phptal:cache should be kept.
setForceReparse(boolean)Forces reparsing of all templates all the time. It should be used only for testing and debugging. It's useful if you're testing prefilters or changing code of PHPTAL itself.
This slows down PHPTAL very much. Never enable this on production servers!