How to make condition, based on custom fields value?

Sorry but it’s not clear what you want to do. From what I understand is you simply want to use an elseif statement:

<?php $pageNumbered=get_post_meta($post->ID, 'page-number', true); ?>

<?php if ( $pageNumbered ) : ?>
    <div class="page-number left">
        <?php echo get_post_meta($post->ID, "page-number", true); ?>
    </div>              
<?php elseif($pageNumbered == "Z") : ?>
    <div class="page-number left">
        <?php echo get_post_meta($post->ID, "page-number", true); ?>
    </div>
<?php endif; ?>

If you can edit you question to be clearer then I might be able to help more.