And a version based on a dispatch table (which is definitely overkill in a simple situation like this):

use strict;
use warnings;

my @input_array = qw( N1 N2 N3  N6  N7      );
my @input_A     = qw( N1 N3 N11 N11 N10 N16 );
my @input_B     = qw( N3 N6 N2  N7  N16 N19 );

my %flags;
$flags{$_} |= 1 for @input_array;
$flags{$_} |= 2 for @input_A;
$flags{$_} |= 4 for @input_B;

my %primaryCCO;
my %dispatch = (
    3 => sub { my $label = shift; print "$label: only 1 input is PI\n"
+ }, 
    5 => sub { my $label = shift; print "$label: this is a wire\n" },
    7 => sub { 
                my $label = shift;
                $primaryCCO{$label} = [1,1];
                print "$label: CCO = ( @{$primaryCCO{$label}} )\n"; 
            },
);

exists $dispatch{ $flags{$_}} and $dispatch{ $flags{$_} }->($_) for ke
+ys %flags;
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