Hi leaveittoblondie,
I'm going to have a shot at answering your question.
The best way to do this is by making an adjustment in the next pay run.
When the time comes to do the next pay run, select New Pay Run from the top right of the Employees tab screen.
Once in the pay run, select the name of the employee you wish to adjust the super for and select the green Actions button and select Adjust Super.
You are now able to put in either a positive number (to increase the super amount) or negative number (to decrease the super amount), then select Save.
You will just need to find out how much the over/under-payment was and plus or minus that in the Adjust Super line that comes up for the pay run.
I hope this answers your question and that you're able to perform this in the system, let us know if you run into any troubles.
Kristian.