Hi Nell,
I have never used the package you refer to but usually there are 2 entries on the Income Tax and NI account. When you prepare your wages calculations, they will show the tax and NI due, this is entered into your accounts package as a liability (CR) .
Then when you pay HMRC you enter this as a payment to the same account - the balance on the account will then be nil.
By the sounds of it you have not done the 1st step but just entered the payment. That is why it looks like HMRC owe you.
:|