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Okay, a couple of things :P
1. Kies Air is an Application for transferring files(like music and pictures) between the phone and computer over a wifi connection.
2. What you were thinking about is a OTA update which is how the phone is usually updated, but for ICS 4.04(I'll assume that's the update you are referring to) you would have to reflash the stock rom, and take off the custom rom.
3. After flashing the stock rom, you'll need to manually connect to a computer with a USB cable, download Kies(PC/Mac software by samsung) and get the update through that, then after the update you can flash another custom rom if you don't like it.
4. I'm not sure, but I think you wouldn't have to reroot, don't quote me though.