How to configure a module after installation
It's up to the module itself to present configuration options, and in Drupal 6 these can be a bit harder to find. I definitely recommend installing the admin_menu module (http://drupal.org/project/admin_menu), which can provide expanding drop-down menus to easily browse through all of the admin-side links.

With cTools specifically, the base 'Chaos tools' module won't do anything on its own, though it can be required by other contrib modules. If you're looking to use one of the bundled modules such as Stylizer or Page Manager, you'll need to enable and configure those modules separately.