Hi Noddy
Desktop does not track or deduct employment allowance automatically. After submitting the EPS as normal it requires a manual liability adjustment to correct the reports withing the software and the steps for this are as follows:
1. Go into Employees > payroll Center > click Pay Liabilities > Adjust Liablities
2. Enter both date and "effective date" (date at which this effects the report)
3. select company and choose the NIC employer item
4. enter amount of employment allowance reclaimed so far
5. Once saved this should now reflect on the reports
