It is my pleasure to inform you that we have released a hotfix for Sitefinity 3.6. You can find it in your Client.net accounts. You can also find the zip file named "External templates" which contains a sample ControlsConfig.xml file with references to all embedded templates, together with the actual templates which should make the process of mapping embedded templates to external ones painless.
http://www.sitefinity.com/support/forums/support-forum-thread/b1043S-bhcgtb.aspx
The major focus of the hotfix was resolving the issues around embedded templates and fixing issues that you have reported after the official release. You can find full release notes here:
http://www.sitefinity.com/support/forums/support-forum-thread/b1043S-bhcgtb.aspx
As a side note, due to large number of inquires about mapping templates and views, I will fast forward with the documentation efforts to the section about ControlsConfig file and once that is done, we'll pick it up with Control Panel class where we have left on Friday.