The Revenue commissioners are correct in their information they relayed to you- by having the pension premium deducted by your payroll department, your PAYE & levies are automatically calculated on the balance of pay (that's the 'net pay arrangement' system at work).
The credits you see on your tax credit certificate are those which are not granted under the 'net pay arrangement' e.g. personal credit, employee credit and any others you might be entitled to claim.
Re the 15% limit, this refers to the maximum percentage of your gross pay that you can currently pay into your pension fund. If you pay a greater percentage, you won't get the tax relief on the excess in the current year. Of course, you can choose to pay a lower percentage.
You should check with your payroll department/ your payslip to see if the 15% threshold is not being exceeded and if necessary advise your payrol department of any required changes.