You use a global variable @modules to pass what modules you want to add to your Perl script. It's better practice to pass in an array to the _makeperl() function with what you want to add. Change:

    if ($addmodule =~ /yes/i) {
        print "\nThis script does NOT add a ';' for you!\nSay 'done' w
+hen you done..\nModules: ";
        while (<STDIN>) {
            last if ($_ =~ /done(;)?/i);
            push @modules, $_;
        }
        _makeperl();
    } elsif ($addmodule =~ /no/i) { _makeperl();}
    else { 
        print "I assume no.\n";
        _makeperl();
    }
[download]

to

    if ($addmodule =~ /yes/i) {
        my @modules;
        print "\nThis script does NOT add a ';' for you!\nSay 'done' w
+hen you done..\nModules: ";
        while (<STDIN>) {
            last if ($_ =~ /done(;)?/i);
            push @modules, $_;
        }
        _makeperl(@modules);
    } elsif ($addmodule =~ /no/i) { _makeperl();}
    else { 
        print "I assume no.\n";
        _makeperl();
    }
[download]

and remove the  my @modules; from the top of the script. Then in your _makeperl() change:

sub _makeperl {
    open (NEWSCRIPT, '>', $name);
    print NEWSCRIPT "#!/usr/bin/perl\n\nuse warnings;\nuse strict;\n";
    if (defined($modules[0])){                  # if module is defined
+, include them to the template
        for my $mods (@modules) {
            print NEWSCRIPT "use $mods";
        }
    }
[download]

to

sub _makeperl {
    my @mods = @_
    open (NEWSCRIPT, '>', $name);
    print NEWSCRIPT "#!/usr/bin/perl\n\nuse warnings;\nuse strict;\n";
    if (@mods){                  # if module is defined, include them 
+to the template
        for my $mod (@mods) {
            print NEWSCRIPT "use $mod";
        }
    }
[download]

Note, I also changed the if (@mods){ which is the usual way of checking if an array has any elements in it.

Similarly you could pass the $name of the script into all the functions as well.