LMCE isn't a torrent download engine (although you can do it) - so it doesn't "handle" them at all in the sense you mean.
You download the files, and put them into whatever directory structure you like under the LMCE media folders. Either locally or preferably on a network share.
The way LMCE presents them to you depends on how you use the UI. You can do it the simple way, and choose Filename sort mode in the media browser and this will display your media using the folder structure you created. Or you can do it the more sophisticated way and tag your media properly - then you can use other sort modes like Performer, Title, Album, etc, and this will then group your media via those attributes and effectively create a "virtual" hierarchy based on the tags.
This sort by tags does not currently include the option to sort by TV series/episode, etc but there has been much discussion of that I and expect that once 0810 is released, someone will add that mode.