They don't show in the URL Manager. If I add 10 new articles, no matter what I do, they will not be listed (I can clear the cache, purge URLs, update URLs, delete ALL URLs and update them again... all I get are the original URLs which were SEFed by Joomla's own engine originally and prior to the installation of JoomSef).
If I disable joomSEF, then it disappears form the site, but I suspect this behavior is by default, since joomSEF is handling the URLs (although undesirable, since it should still show my articles whether JoomSEF is active or not)