You will not receive an outright payment of £3,000( for 2016-17 tax year) from HMRC, however under the scheme you can reduce the amount of Employer NICs you pay over to HMRC each month/quarter by up to £3,000.
Once you have set up your Employer Allowance Claim, the reduction in your Employer NIC liability to HMRC will be automatically calculated and shown in column 6 of your Employer Payment Record (P32 replacement) and your payment due to HMRC each month/quarter will be shown reduced accordingly. The £3,000 claim will be a reducing balance over time. i.e. the £3,000 claim will be offset against your Employer NIC liability to HMRC until the £3,000 is used up. Your full Employer NIC liabilities will continue to be detailed on payslips and other reports.
Once the £3,000 has been used up the claim will automatically stop. You do not need to tell HMRC that you are stopping the claim unless you are stopping the claim early before the full £3,000 has been been claimed.
Road Map - To view Employment Payment Record (P32 Replacement)
Reports -> Payslips, Payroll and PAYE -View/Print-> Employer Payment Record (P32 replacement) link
( 'Reports' is the button positioned in the tasking zone menu at the top. It is the second button from the right)
Finance -> Pay HMRC (Tax & NI) ->Employer Payment Record EPR (P32 replacement) -> View P32 link
( 'Finance' is the button positioned in the tasking zone menu at the top. It is the third button from the right)