in the interest disclosure it will simply say something about the average daily balance and that amount, once it is added in is part of your average daily balance.
And why are you worried about a credit score? Read the book. Keeping the account open and paying them $99 a year for something you will probably never need is ridiculous. You have 30 days to protest the fee and if they just started adding it then they can’t keep charging you. Call them and close the sucker.