i actually got a 200gb seagate HD for x-mas too, and i had some problems with it, but i was making it my boot HD.
If you want it as your slave drive, make sure the correct IDE cables are in each drive, (you say u did), and that a jumper is in the main drive to make it master, and no jumpers are in the 2nd drive to make it slave, (you say u did). So, after that, if u can boot up on your main old HD, and your not seeing the new drive? (i think this is ur problem), you have to partition your new harddrive for it to be recognized to have any storage on it.
"Then I booted up and windows tells me there is a major change in my harddrives so I have to register again."
-This makes it sound like the drives wern't configured correctly with jumpers and IDE cables.
If you say the slave part of the IDE cable wont work, try gettin a new cable, or a cable you know worked before, and put it in there. You should be able to have 4 IDE devices for 2 cords. On each cord, a master/slave.