One way you can do it is :
Edit the index.php from here /templates/ja_teline_ii/ and :
replace this code :
<h1 class="logo">
<a href="index.php" title="<?php echo $siteName; ?>"><span><?php echo $siteName; ?></span></a>
</h1>
with this one
<object">
<param name="movie" value="logo.swf">
</param>
<embed src="<?php echo $tmpTools->templateurl(); ?>/images/logo.swf" height="XXX" width="YYY"></embed>
</object>
You will have to upload your flash logo to /templates/ja_teline_ii/images and set the width and height accordingly to your template (see the red X and Y)
Good Luck.