Special episodes and extras are put in a separate season folder called 'Season 0' or 'Specials' inside the series folder. You then use the same naming convention as the main episodes but use S00Exx. The TV info for each episode is imported from the information held at
www.thtvdb.com.
So, for instance from my library taking 'The Big Bang Theory' as an example. I have the folder structure set up as follows:
The Big Bang Theory
---Season 1
------The Big Ban Theory.S01E01.mkv
------The Big Ban Theory.S01E02.mkv
------The Big Ban Theory.S01E03.mkv
------The Big Ban Theory.S01E04.mkv
------The Big Ban Theory.S01E05.mkv
---Season 2
------The Big Ban Theory.S02E01.mkv
------The Big Ban Theory.S02E02.mkv
------The Big Ban Theory.S02E03.mkv
------The Big Ban Theory.S02E04.mkv
------The Big Ban Theory.S02E05.mkv
---Specials
------The Big Ban Theory.S00E01.mkv
------The Big Ban Theory.S00E02.mkv
------The Big Ban Theory.S00E03.mkv
------The Big Ban Theory.S00E04.mkv
etc, etc
The special episodes will then appear in 'Season 0' for the relevant show in MC.
If you then look at
http://thetvdb.com/?tab=series&id=80379&lid=7 and select the specials season you will be able to see what episode number each entry has to be.
If there is an entry in TVDB for your episodes then the entry in MC will reflect that and if there is no entry for a given episode then it will just be labelled as 'Episode xx' in MC
Any episodes that don't have an entry in TVDB you can manually edit the 'Name' tag in MC.
I hope this helps but just ask if you want any more clarification.