Quick answer
Agency charges can be separate from the original ticket fine.
Do now
Verify the bill through the issuing agency. Review the underlying convictions, calculation period, payment options, and dispute process. Compare with your driving record and keep payment receipts.
Watch for
Paying the court does not necessarily pay the agency assessment. A point-reduction course may not eliminate a separately imposed assessment. Use current instructions rather than an old fee table.
Official sources
NJ MVC — Surcharges, NY DMV — Driver Responsibility Assessment, NY DMV — How to Keep Your License.