First thing you need to do is set up Hammer to accept the EX mapping systems, to do this i suggest going here:
http://83.169.21.186/40ksource.com/common/wiki_manual/index.php?title=Mappingand reading that.
In the MDK2 folder where it was installed there are models and 2 test maps you can have a look at. a selection of these models are doors that both a space marine and a duckeed nid warrior can walk through, these are your best bet to base the sizes of things from.
The demo maps you can look at are located here:
C:\Steam\steamapps\SourceMods\ex_dev\mapsrc
and the models and the like here:
D:\Steam\steamapps\SourceMods\ex_dev\models\props
the models can be viewed with the model viewer in the source SDK.
Only thing remeber that the carnifex is VERY large and will need more room.
Should you have issues gettign the setup of EX to work, then build what you can first using the basic half life 2 stuff as a starting point, good tutorials can be found here:
http://www.editlife.net/tutorial.php?tutid=22Shoudl you still have problems, please ask us for more advice, i can send you a simple 2 room map for you to look at to get sizes if you need it.