First of all, there are the generic HTML::Template options (using a <tmpl_include>, for instance). See the recent article on Perl.com, Advanced HTML::Template: Widgets.

CGI::Application offers several ways to help implement this. My first choice would probably be the load_tmpl hook. It would allow you to set the required variables whenever you load your main template:

sub navbar_callback {
    my ($self, $ht_params, $tmpl_params, $tmpl_file) = @_;

    if( $tmpl_file eq 'master.tmpl' )
    {
        # load your variables
        my %navbar_params = $self->navbar_params;
        $tmpl_params->{$_} = $navbar_params{$_} foreach keys %navbar_p
+arams;

        # alternatively, you could also load a separate template for t
+he navbar, and
        # pass it on to the master as a tmpl_var. Note that the if() c
+lause protects you
        # from an infinite loop
        # $tmpl_params->{navbar} = $self->navbar_template;
    }
}
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You turn this callback on in e.g. cgiapp_init or setup:

sub setup {
    my $self = shift;
    $self->add_callback( 'load_tmpl' => 'navbar_callback' );
}
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Now every time you call $self->load_tmpl('master.tmpl'), the navbar will be filled automatically.

Another approach I used before the callback infrastructure was available, was to use the cgiapp_postrun method to fill in the bits and pieces: every run mode would only return the output specific to it, while the cgiapp_postrun would stitch the pieces together into the overall page. I did this by loading the master.tmpl, passing it the runmode output as a var, and loading other generic stuff as well:

sub cgiapp_postrun {
    my ( $self, $outputref ) = @_;

    # the following conditionals protect us from trampling on
    # 'redirect' runmodes, or non-html output.
    if( $self->header_type eq 'header' ) {
        my %props = $self->header_props;
        if( !exists( $props{'-type'} ) or $props{'-type'} eq 'text/htm
+l' ) {

            my $t = $self->load_tmpl('master.tmpl');

            $t->param( runmode_content => $$outputref );
            $t->param( navbar_content  => $self->navbar_template );

            $$outputref = $t->output;

        }
    }
}
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