Ok, I've read through everything and want to answer a few old questions before beginning, or at least clarify some things.
First, someone mentioned ilovebees not making it canon wise. However, Bungie employee Frank, while discussing the Graphic Novel, said that ilovebees is held as canon by Bungie.
Second, I think this was mentioned before, but the Spartan 1s did not fight against the Covenant for the UNSC. They were disbanned before the war.
Now, as for the questions asked at the beginning.
1) I would imagine they were stationed on different defense platforms. If you had all 4 Spartans on Cairo Station and it was soundly held, the Covenant would destroy all the others and still take Earth with ease. Thus, the Spartans were probably spread amongst the stations. However, I do not believe any Spartans were on Malta Station or Athens Station because they were both very near to Cairo Station and it would make more sense to spread the Spartans wider out as even holding 4 Stations is pointless if they all can see the same thing and the rest of the planet is defensless.
2) I personally tend to agree with the speculation that Dr Halsey took Kelly to the star-coordinate found in Ackerson's files. Some speculate that this is where Mendez is training Spartan-IIIs, and I lean towards this speculation.
3) I also believe that the Covenant found the Earth through a "trail of breadcrumbs", as it was so aptly put earlier in this thread, in their never ending search for Forerunner artifacts. In fact, concerning the whole war, I think the Covenant view the UNSC as a pest and only truly engage them when looking for an artifact. The Covenant aren't hunting and exterminating the humans, they are killing any non-Covenant beings in their search for the Forerunner. In essence, I don't think the Covenant regaurd it as a war as much as perhaps a search with minor obstacles. The fact that the Covenant are left in civil war and are beginning to lose to the UNSC at the end of Halo 2 means that they may start taking the UNSC threat seriously. However, during the first contact with the Covenant, the Covenant made mention of a holy war against the humans, and they said it in English, which implies they have been watching us. Also, I can't remember where it is mentioned, but in a conversation between some Covenant (I think they were grunts in Conversations of the Universe) it mentions that all races before the humans were given the option of assimilation, whereas the humans were not. These point to another reason for the Covenant destroying the humans, but I still think they don't take us seriously. We are neither enough in numbers to be fodder like the grunts and jackals nor are we strong enough to fight without weapons like the brutes and hunters (with exception to the Spartans) nor are we technilogically advanced enough to be considered an intelligent race like the elites, prophets, and engineers.
I like pi.