You can change it so that the reply panel appears with your site layout.
Create a new template named my-comments-reply-tpl.php. Insert your page header, sidebar and footer HTML. Then copy the below code into the template.
In the head section of the page:
<?php require 'head-inc.php'; $separator = ($location[0]) ? '–' : ''; ?>
In the body section of the page:
<?php
print "
<div id='tb-wrapper'>
<div id='ID-$tbid[0]' $comment_type_class[0]>
<div class='$header_class[0]'>
<div class='$author_loc_class[0]'>
<span class='$author_class[0]'>$author[0]</span>
$separator
<span class='$location_class[0]'>$location[0]</span>
</div>
<!-- <div class='$tbid_class[0]'> | #$tbid[0]</div> -->
<div class='$date_class[0]'>$time[0]</div>
</div>";
if ($config['comment_subject'])
// Show subject line
print "
<div class='tb-comment-subject'><span class='tb-subject-title'>{$lang['subject']}</span> $subject[0]</div>";
print "
<div class='tb-comment-text'>$text[0]</div>
</div>";
// +++++++++++++++++++++++++++++++++++++++++++++++
// Print the comments entry form
// +++++++++++++++++++++++++++++++++++++++++++++++
print "
<p class='tb-stress'>{$lang['reply_panel_legend']} {$author[0]}</p>";
require COMMENTS_FORM_TPL;
print "
</div> <!--end of tb-wrapper -->";
?>
Finally, change the reply panel file name in the admin configuration settings panel.