I found a solution that works exactly how I want.
I changed
$this->form_validation->set_rules('name', 'Name', 'trim|required');
$this->form_validation->set_rules('code', 'Code', 'trim|required');
$this->form_validation->set_rules('userfile', 'Document', 'required');
To
$this->form_validation->set_rules('name', 'Name', 'trim|required');
$this->form_validation->set_rules('code', 'Code', 'trim|required');
if (empty($_FILES['userfile']['name']))
{
$this->form_validation->set_rules('userfile', 'Document', 'required');
}