First Skynet sent the T-1000 back to 1995 to kill John Connor. Then, when John Connor still existed, it jumped to the conclusion that the T-1000 must've failed. The idea that a T-1000 would fail to kill a ten year old boy was unthinkable, so it must've concluded that its information about John's whereabouts in '95 was incorrect. That left only one more piece of information to act on: the fact that Sarah Connor lived in L.A. in 1984. Since it had no other T-1000s to send, Skynet instead sent a T-800 to kill her.
After that, the resistance smashed Skynet's defence grid and captured the Time Displacement facility. John knew he had to send Kyle back in time to protect Sarah, so he did so. But for some reason he didn't tell Kyle anything about the T-1000, or about the other Terminator that John himself would send back. I suppose you could rationalize this by saying that John didn't want to answer too many awkward questions about where Kyle would be by that time, or where John's father would be while the T-1000 stalked him, but the real reason is that Cameron just didn't plan ahead when he wrote Kyle's dialogue in the first movie. In any case, once Kyle had been sent, John told his sapper team to hold off on setting their charges because he had one more thing to do. (He also commented offhandedly that Kyle was his father.) He then went into the Terminator storage freezer which contained racks upon racks of Terminators. Each rack held a different model of Terminator, but there were ten of the same model per rack. John kept looking until he found a rack with one empty space, but with very familiar features on the remaining nine Terminators. He then took one of those nine, reprogrammed it, and sent it back to 1995.
Incidentally, the first paragraph above is speculation, but the second paragraph is based on a scene from the original rough draft of the script, which was included on the T2 Ultimate Edition DVD, and on the novelization that was based on it. If you'd be interested in a more heavily speculative account, including the idea that the T-1000 may not have been the first Terminator sent back, then check out my thread here: http://www.imdb.com/title/tt0103064/board/thread/255586950 It hasn't gotten much response yet, but that's probably because it's a pretty big wall of text even by my standards. You have been warned.
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