As you can see, a Nayrulian cannot see what goes on in Din and Farore, and vice versa. The Temple of Light and Dark is the place where members from all the clans can meet and have chit-chat about various things. There are forum games within, and also a huge community thread (that is actually sorta dead at the moment). It's like the Lounge of Nayru, it's just meant for every clan members.
The Clan Arena... There used to be clan wars in the summer - that will probably come back to life as soon as school ends. Now it is dead also. So you go to the Clan Arena when you want to see the results / contests of the clan wars' rounds.
In Zelda RPG you can obviously roleplay in the world of Zelda. So the characters are Zoras, Gorons, Deku Scrubs and Sheikahs and so on. To join the roleplaying, you must make a character there (you post a thread with describing your character's name, occupation, race, age, appearance, abilities, strengths and weaknesses, history, etc.), and then you must post from the perspective of your character, and thus join the adventures around Hyrule.
As for the X-clan... I don't know that either, so it must be an inside joke, or something. Anyway, hope I could help. :3