Thank you VERY much for that. I am a beginner, and therefore before I make so many changes I would just like to run by you a few things if that's OK? When you talk about cloning, does this mean making a copy of each relevant line within each relevant file, and renaming from 'comments' to 'comments1' for example?
If so, where in the files do I put the copy, immediately after each original line in each original file? If there are a group of lines together in a file, do I clone the whole group, or one line at a time? Sorry, these questions might sound just dumb to you, but for me in Wild West Wales things aren't quite as obvious! 
The lines or references that I think are relevant after getting rid of the ones you advised are as follows. If anything looks wrong, please let me know. Many Thanks:
HTML Code:
[B]/var/www/html/includes/classes/order.php[/B]
Line #341 : 'comments' => (isset($_SESSION['comments']) ? $_SESSION['comments'] : ''),
Line #633 : 'comments' => $this->info['comments']);
Line #897 : //comments area
Line #898 : if ($this->info['comments']) {
Line #899 : $email_order .= zen_db_output($this->info['comments']) . "\n\n";
Line #900 : $html_msg['ORDER_COMMENTS'] = nl2br(zen_db_output($this->info['comments']));
Line #902 : $html_msg['ORDER_COMMENTS'] = '';
[B]/var/www/html/includes/languages/cymraeg/checkout_confirmation.php[/B]
Line #20 : define('HEADING_ORDER_COMMENTS', 'Cyfarwyddiadau Arbennig neu sylwadau Archeb');
Line #21 : // no comments entered
Line #22 : define('NO_COMMENTS_TEXT', 'Dim');
[B]/var/www/html/includes/languages/cymraeg/checkout_payment.php[/B]
Line #22 : define('TABLE_HEADING_COMMENTS', 'Cyfarwyddiadau arbennig neu Sylwadau Archeb');
[B]/var/www/html/includes/languages/cymraeg/checkout_shipping.php[/B]
Line #25 : define('TABLE_HEADING_COMMENTS', 'Cyfarwyddiadau Arbennig neu sylwadau ynglyn a\'ch archeb');
[B]/var/www/html/includes/languages/cymraeg/checkout_success.php[/B]
Line #20 : define('TABLE_HEADING_COMMENTS', '');
[B]/var/www/html/includes/languages/english/checkout_confirmation.php[/B]
Line #20 : define('HEADING_ORDER_COMMENTS', 'Special Instructions or Order Comments');
Line #21 : // no comments entered
Line #22 : define('NO_COMMENTS_TEXT', 'None');
[B]/var/www/html/includes/languages/english/checkout_payment.php[/B]
Line #24 : define('TABLE_HEADING_COMMENTS', 'Special Instructions or Order Comments');
[B]/var/www/html/includes/languages/english/checkout_shipping.php[/B]
Line #25 : define('TABLE_HEADING_COMMENTS', 'Special Instructions or Comments About Your Order');
[B]/var/www/html/includes/languages/english/checkout_success.php[/B]
Line #20 : define('TABLE_HEADING_COMMENTS', '');
[B]/var/www/html/includes/modules/pages/checkout_confirmation/header_php.php[/B]
Line #44 : $_SESSION['comments'] = zen_db_prepare_input($_POST['comments']);
[B]/var/www/html/includes/modules/pages/checkout_payment/header_php.php[/B]
Line #90 : // $_SESSION['comments'] = '';
Line #91 : $comments = $_SESSION['comments'];
[B]/var/www/html/includes/modules/pages/checkout_process/header_php.php[/B]
Line #25 : unset($_SESSION['comments']);
[B]/var/www/html/includes/modules/pages/checkout_shipping/header_php.php[/B]
Line #122 : if (isset($_SESSION['comments'])) {
Line #123 : $comments = $_SESSION['comments'];
Line #129 : if (zen_not_null($_POST['comments'])) {
Line #130 : $_SESSION['comments'] = zen_db_prepare_input($_POST['comments']);
Line #132 : $comments = $_SESSION['comments'];
[B]/var/www/html/includes/templates/classic/templates/tpl_checkout_confirmation_default.php[/B]
Line #87 : // always show comments
Line #88 : // if ($order->info['comments']) {
Line #91 : <h2 id="checkoutConfirmDefaultHeadingComments"><?php echo HEADING_ORDER_COMMENTS; ?></h2>
Line #93 : <div><?php echo (empty($order->info['comments']) ? NO_COMMENTS_TEXT : nl2br(zen_output_string_protected($order->info['comments'])) . zen_draw_hidden_field('comments', $order->info['comments'])); ?></div>
[B]/var/www/html/includes/templates/classic/templates/tpl_checkout_payment_default.php[/B]
Line #200 : <legend><?php echo TABLE_HEADING_COMMENTS; ?></legend>
Line #201 : <?php echo zen_draw_textarea_field('comments', '45', '3'); ?>
[B]/var/www/html/includes/templates/classic/templates/tpl_checkout_shipping_default.php[/B]
Line #118 : <fieldset class="shipping" id="comments">
Line #119 : <legend><?php echo TABLE_HEADING_COMMENTS; ?></legend>
Line #120 : <?php echo zen_draw_textarea_field('comments', '45', '3'); ?>
[B]/var/www/html/includes/templates/template_default/templates/tpl_checkout_confirmation_default.php[/B]
Line #87 : // always show comments
Line #88 : // if ($order->info['comments']) {
Line #91 : <h2 id="checkoutConfirmDefaultHeadingComments"><?php echo HEADING_ORDER_COMMENTS; ?></h2>
Line #93 : <div><?php echo (empty($order->info['comments']) ? NO_COMMENTS_TEXT : nl2br(zen_output_string_protected($order->info['comments'])) . zen_draw_hidden_field('comments', $order->info['comments'])); ?></div>
[B]/var/www/html/includes/templates/template_default/templates/tpl_checkout_payment_default.php[/B]
Line #200 : <legend><?php echo TABLE_HEADING_COMMENTS; ?></legend>
Line #201 : <?php echo zen_draw_textarea_field('comments', '45', '3'); ?>
[B]/var/www/html/includes/templates/template_default/templates/tpl_checkout_shipping_default.php[/B]
Line #118 : <fieldset class="shipping" id="comments">
Line #119 : <legend><?php echo TABLE_HEADING_COMMENTS; ?></legend>
Line #120 : <?php echo zen_draw_textarea_field('comments', '45', '3'); ?>