While editing your article, your links will look like "index.php?option=com_...". But once you publish it, and you browse to that article in the front end, the link will be replaced by the proper SEF URL automatically.
Linkr 2.3.8 (13 June 2011) is ready for download, and is compatible with MooTools 1.2. It has also been tested with the Firefox 4, Internet Explorer 9, and Google Chrome browsers.