You cannot only set rules in the config/form_validation.php file. You can also set them with:
$this->form_validation->set_rules();
More info on: http://codeigniter.com/user_guide/libraries/form_validation.html#validationrules
However, the order of preference that CI has, is to first check if there are rules set with set_rules(), if not, see if there are rules defined in the config file.
So, if you have added rules in the config file, but you make a call to set_rules() in the action, the config rules will never be reached.
Knowing that, for conditional validations, I would have a specific method in a model that initializes the form_validation object depending on the input (for that particular action). The typical situation where I've had the need to do this, is on validating shipping and billing addresses (are they the same or different).
Hope that helps. :)