Well you could either manually add the thumbnail image tags to the link_summary.tpl file or wrap a <div> around the thumbnails using Upload Module settings page. The "HTML code to place before the Thumbnails" and "HTML code to place after the Thumbnails" fields are there so that you can wrap some <div> around the automatically embedded thumbnails.
Here's a quick example to float all uploaded thumbnails to the right of the article by using the Upload module settings page.
Where to embed thumbnails: tpl_link_summary_pre_story_content
HTML code to place before the Thumbnails: change the width value to match the width of your thumbnails. Alternatively you could alter the "Manual Thumbnail HTML format" field so that images will better align themselves.
Code:
<div style="float:right;margin:0 0 6px 10px;width:200px;">
HTML code to place after the Thumbnails:
Manually place this code in link_summary.tpl just before your story tools section:
Code:
<div style="clear:both;"> </div>