The original place for the Catholicos was at Etchmiadzin, something which is touched on in this post in the OO music thread:http://www.orthodoxchristianity.net/forum/index.php/topic,9840.msg443024.html#msg443024
I'm far from being an expert on these things, but this is the history as best I understand it:
Because of the tumultuous history of the area, the Catholicosate (is that the right word?) had to move several times. I think a couple of the earlier places it moved to were Dvin and Ani. At one point the Catholicos was at Akhtamar, before moving to Cilicia. In fact, after the Catholicosate moved from Akhtamar, the people of Akhtamar still wanted a catholicos, so one continued to exist there up until the time of the Genocide.
Eventually, the Catholicosate moved to Cilicia and was there for a few hundred years. This was during the Crusades, and during that time that the Catholicos united the Church with the Roman Catholics, a move which the Vartabeds in Greater Armenia vehemently opposed. Finally, in the fifteenth century, an agreement was reached that said when the Catholicos in Cilicia died the new Catholicos who replaced him would be up at Etchmiadzin. So the Catholicos in Cilicia died, and a new one was installed in Etchmiadzin.
The problem was that the people of Cilicia, like the people of Akhtamar, wanted to still have a catholicos. So even though the new Catholicos was installed at Etchmiadzin, the Armenians in Cilicia went ahead and installed a new Catholicos for themselves, and a Catholicosate continued to exist there.
Is this making sense? If it isn't, don't worry.
Anyway, at the time of the Genocide there were really three catholicoi: Etchmiadzin, Cilicia and Akhtamar. In addition to that, there were two Patriarchs at Jerusalem and Constantinople. The Catholicoi at Cilicia and Akhtamar had local jurisdiction where they were, but the Catholicos of Etchmiadzin was (and still is) universal. The Patriarchs of Jerusalem and Constantinople, for example, have their bishops ordained at Etchmiadzin, and they get their muron from Etchmiadzin.
At the time of the Genocide, the Armenians of Akhtamar and Cilicia were slaughtered. The Catholocosate of Akhtamar ceased to exist, but the Catholicosate of Cilicia was eventually able to reestablish itself in Antelias, Lebanon.
So that is why there are two Catholicoi today in the Armenian Church, one in Etchmiadzin and one in Antelias. With regard to your question as to which is the "real 'Catholicos of All Armenians,'" Etchmiadzin has traditionally been recognized as having universal jurisdiction. As noted above, both Patriarchs of Jerusalem and Constantinople have their bishops ordained at Etchmiadzin, etc. However, with the existence of the diaspora after the Genocide, there have been issues raised as to which catholicos has jurisdiction over the Armenians in diaspora. That is why in most places here in the U.S. with an Armenian community, you'll see two sets of Armenian churches: some under Etchmiadzin, and some under Cilicia (Antelias.)
I have to stress, though, that having all these different catholicoi has never been a cause for excommunication. All the catholicoi and patriarchs are in communion with each other. Our bishops concelebrate, and Armenian laypersons can take communion in both churches without a problem.