When you make the final submission for a tax year this must be done from the global HMRC Workbench, because the declarations cover all employees, regardless of their pay frequency.
If a submission that is marked as a final submission has been made, and you make a further submission in the same tax year on one of the frequency-specific workbenches, the "Final Submission" box will be ticked.
If you have submitted your final FPS (and where appropriate an EPS) for the tax year, but haven't indicated that this is your 'Final submission for the tax year', you must submit an EPS indicating that it is your 'Final submission for the tax year'.
To make an end of year declaration:
Go to HMRC Workbench.
Create the FPS (or EPS) record.
Tick the Final Submission for Year box.
If the PAYE scheme has ceased, enter the date the scheme ceased.
Click save to save the return record.
Submit the return as usual.