I don't think you're going to be able to get that, nice and neat, on the check out report. The only thing I could think of is that you can ring it in as an item, then check on the product mix report on BOH before checking out the server, and see how many times the 1.99 item was rung in. Then deduct that total from their cash owed. The problem with that is, it will throw off the entire deposit, unless you maybe enter it as a paid out. I can't think of any solution thats going to be pretty.
On a side note, I don't know if you guys had done this in the past (it was hard to tell from your post), but get ready for the backlash from the custoemrs.
I know you it's not your decision, and personally I am too loose with my money to probably even notice this was on the bill- but a lot of people are going to have a BIG problem paying 1.99 to get their individual total (splitting a check). I'm not sure why, but I would almost feel more annoyed if I knew the money is going to the server-she is already being paid to do her job, by the restaurant and by my tip.
I always thought split plate charges were pretty questionable, but this doesn't really fall under the category of "special request" that you can charge more for. When you eat at a restaurant, you should expect to get the total you owe and expect to pay that total-not pay to get the total itself.
Not only that, I am fairly certain that this is NOT legal in your state. Might wanna check (but it will cost you a 1.99 to ask them-lol).
Anyway, please don't take it personally, just giving you a heads up.