You can define additional payments in payroll software to show up in payslip and mark them as subject to tax, NI & Pension or not. Once done then all that can be accounted for in payroll journals
Thank you @Accountant, but…
Would I be right in thinking these costs would be moved to the correct nominal account in the payroll journal, either by the software (in my case, the payroll site), or manually?
In terms of proof of travel expenses then (hotels, fuel etc.), is there a way of linking them to the journal as proof, or just keep a digital copy on the account?