It can be confusing so don't beat yourself up too much :)
There are two ways of working out NIC calcualtions and I've detailed this below:
This method is used to calculate NI on total earnings to date each time a Director is paid they receive an NI free amount, currently £8,632 and pay NI on any amounts above this threshold. This method is normally used for Directors who receive irregular amounts.
April - £5,000 - No NIC
June - £5,000 - NIC Payable as below
Total pay to date = £10,000. NIC Calculated on £10,000 minus £8,632 (NIC free amount) = £1,368.00
NIC due on £1,368 @ 12% = £164.16.
Employer NIC due on £1,368 @ 13.8% = £188.78 to pay to HMRC for period
August - £5000 - NIC Payable as below
Total pay to date = £15,000. NIC Calculated on £15,000 minus £8,632 (NIC free amount) = £6368.00
NIC due on £6368 @ 12% = £764.16.
Deduct NIC already paid of £164.16 = £600 to deduct.
Employer NIC due on £6368 @ 13.8% = £878.78 minus £188.78 already paid leaving £690.00 to pay to HMRC for period.
Non Cumulative/Alternative Method:
For this method, NIC is calculated much like an employee, on each pay packet.
This means that the monthly threshold rather than the annual threshold is used to calculate payable NIC e.g.
April - £1,000
£1,000 - £719 = £281
£281 @ 12% = £33.72 to deduct
With both methods I would always perform an NIC check using the HMRC calculator before the final pay of the year is processed to ensure that the correct amounts have been deducted, available via the below link: