Paycheque paid from 2 accounts

SUGGESTED

I have a client who consistently will pay one employee from two separate accounts.  Eg. We create a cheque for 3500.  she will pay 3000 from one account and 500 from another account.  The cheque is produced on acct 1. So if this happens at the end of the month, then 500 of it is outstanding in acct 1.  Easy.  Then I get the bank statement and see she paid the remainder out of the second account.  I am sure this is easy, but I am stumped.