If I am creating a payslip for an employee to pay for salary and a reimbursement, I would use two lines one for the salary and one for the reimbursement, correct? the salary i would put under employee clearing account and what would i put the reimbursement under?

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If the employee spent his/her own money on a company expense, that should have been recorded via an expense claim. So the reimbursement is allocated to Expense claims and the employee’s subaccount.