Pay employee's claim using payroll

Don’t record it on both. First, make sure you have read and understand the Guide below:

If you have entered your employee’s expense claim using their name as it appears in the Employees group, the amount you owe them will be added to the Employee clearing account. You cannot, in fact, enter it directly as a payslip item. When you pay the employee, Spend Money from a cash account and pay them the full amount you owe, including both the payslip (without any expense claim) and the expense claim, that shows under Employees tab.

The important thing to understand is that the payslip records the amount you owe for work done. The expense claim records the amount you owe for company expenses the employee paid from personal funds. They might be combined into a single check, but they are separate things.