I just went through this less than a month ago with my wife's line, plus I also did the same thing (buy out) with my own line. My line was $50 to buy it out..wife's was $100 to buy out.
The mix-up is coming in when you call a Sprint store. First time, with my line, they said that the $50 would be added to my next bill. Paid in-store for the phone though, $199.
My contract on that line was due up at the end of July, so as of August 1st, had I waited, I would've been able to get the contract price, but I got my SGS3 on July 19.
Her's was due to be renewed on November 1...we got her upgrade on September 5 or so..it was $100. I asked about my 3rd line, which isn't due for an upgrade until December 1..they said that one would be $175...
so it all depends on how long is left in your current contract. And depending on the store, they may/may not put the buy-out fee on your bill. When we did my wife's phone, we went to the same store, and we had to pay the $100 in-store, instead of it being put on my bill. Not sure why, and didn't really say much about it..either way I still had to pay it.