for anyone else looking for the directory into which you should upload a javascript file it is
yoursite.com/wp-includes/js
just remember to add the correct url to the tags calling the script within your head tags
you need to edit the header.php file of your template to add the logo and the link.
(apologies if you know html already) by adding the right locations to this code
<a href="http://site you wish to link to"><img src="http://location of the logo you want to show up"></a>
you will need to place this in the same header div, but you may need to alter the css to position in correctly – sorry I don’t have acess to the thesis theme to give you the exact code you need
