Preferance? comment_form or comments_template

If I use <?php comment_form(); ?> comments disappear from the Theme. Any ideas?

Those two functions do entirely different things. A theme should have both of them.

The comment_template() function both loads the comments from the database and loads the comments.php file in the theme to display them.

The comment_form() function displays the comment form. It would be located in the comments.php file.