You basically got this answer form someone else already I think, but here is how I do it. I use a single Template for the bulk of my page - with the exception of a form. This particular project already has 150 or so forms.

    my $page = $self->load_tmpl('page.tmpl');
    my $form = $self->load_tmpl('ap_qsign.tmpl', die_on_bad_params => 
+0);
    $form->param($errs) if ref $errs;
    $page->param('form_text' => $form->output());
    return $page->output();
[download]

This is from an app based on CGI::Application. The two templates get loaded, in the form template the VAR substitution is done, then the output of the form is substituted in a normal TMPL_VAR, in this case form_text and then the output of the combined objects is returned and output.

Going back to your original question, the Problem of pointing to template directories is interesting. I had forgotten about it entirely because CGI::Application gives us a tmpl_path method that sets the template location.

Good luck!
jdtoronto