One way is to open each student, reconcile the account, and make an adjustment of $1000. anything else will be deducted through payroll.
A second way is to enter the amount as a negative number in the column "Fine After Taxes." This will avoid the taxes, and the negative fine becomes a positive number. Enter $1025 so that Union dues are covered if you have them. This will result in a paycheck of $1000.
In real life, when we get a "signing bonus" because we start working for a company, we still pay taxes, so you can adjust the amount to $1250 and have them pay taxes.