This i did end up figuring this out, mind you its the same work around every other doco aficionado landed on. Considering how many times this post has been viewed since its inception i should note the solution.
The solution is probably only one of many to be found but it works for me. It involved a relative amount of manual sorting, to avoid that in the future i'll try to make sure i download doco sets. Which tend to be more prevelant on thetvdb.com
Firs, this workaround only applies to Aeon MQ series skins as thats the only one i use. Using any other skin with not as much menu customization will still be possible but more complicated.
Second, this solution implies you have named your Doco series under the naming convention of thetvdb.com and your series are infact listed on thetvdb.com
Like all good libraries the solution to seperating your Doco's from your movies or TV show menu's starts with where and how you store the video files. Mine are stored in the folders >Tower\Documentaries\Series\100 Greatest Discoveries\1x02 Biology etc etc. Just as you would store your TV Shows.
Then its simply a matter of navigating XBMC to main menu > Video > New Smartlist. Set the type as TV Shows, Name the playlist (whatever you like) Rule 1: Find items where: Path Contains: Series (Note this is the same name as the folder that stores my doco series. Limit to: No Limit Order By: Episodes - Descending. Hit the Add button and then navigate to XBMC main menu > Video > Files.. > Add Video. Navigate to your respective location that holds your doco files and add that location.
After that all you need to do is navigate XBMC main menu > Settings > Skin > Shortcuts/Backdrops. Here you need to scroll over to VPlaylist > activate > Add video playlist. Select the .XSP (smart playlist file) you just created, Rename the menu option Doco's or something and your done.
This will not however seperate your doco's from your main TV Show menu. If you want to keep this TV show menu clean then you must create the same VPlaylist but for your TV Shows, (and obviously add the location as we did with the doco's). So now you have two TV Show main menu items...what the? Go into settings > skin > Shortcuts/Backdrops and deactivate the originall TV Show menu item, say goodbye to your "recent Tv Episode widget" and have a good night. Nobody said workarounds are perfect.