This can be recorded against a staff members contract. Please note you will need the human resources user role to do this.
To do this locate the staff's profile by going to Admin > Personnel > Staff and select the staff member in question. On the profile click the cog next to the contract you need to record this against.
In the contract edit area scroll to the very bottom and beneath the delete contract option you'll see the area to record the additional payment.
Fill out the information and click add payment. Once this is added it will show on the left of the contract information.
Please be aware you cannot edit the additional payments when added therefore if you need to amend this you would delete the record using the little red cross and re add the payment.