Our company paid for a flight for an employee with the agreement that the employee would repay half. 
The full amount was paid with the company credit card.

I posted a purchase invoice for the flight paid by the credit card. Then the repayment was posted by posting a negative amount to the reimbursement line on his payroll cheque. 

The problem is the reimbursement account is balancing. How should I have posted this and can I fix it?