2 pay cycles paid as one

Hello, 

My company pays the employees on a fortnightly basis. 

There is this one employee who was paid for 2 pay cycles as one sum-payment for this month. 

To put this in an example, say, There is X. X receives $1000 every fortnight. X didn't receive his pay for the first fortnight. When he completed his second fortnight, he received a sum $2000. This amount covers the first and second fortnightly pay cycle. 

Here is where the problem arises. The bank feed shows a withdrawal amount of $2000. I have two payslips, one for each fortnight i.e., $1000 each. MYOB won't let me link the $2000 with the two payslips. It has to be a single payslip apparently. 

How would I be able to fix this? Please help. 

Sincere regards, 

Gemes