I think you might be missing some information in your description of the problem.  From my perspective, if you, as you said you did, dated the cheques Sep 1, paid the employees on Sep 1, then how can an employee get to the bank, cash the cheque and have the banking system get it back to your bank to clear your bank account the month before you even released the cheques?

Yes, sorry. I use a credit union direct deposit system, so I manually enter into that for direct deposit on September 1st. The entire summation of cheques deposited are withdrawn from our bank account on August 29th, deposited to employee September 1st. 

Some will argue for different approaches here but my best advice is to set up a clearing account for your payroll cheques that is used as the linked account for your payroll module.

When you process each cheque for that future date (eg. Sep 1), it will be withdrawn from that account and will show on the balance sheet as a negative balance in the account.

When you see the money removed from your bank account (eg. Aug 29), you can post a general journal entry to remove the money from the bank account decreasing it's balance (credit) and then posting the other side (debit) to the clearing account to increase it's balance.  By Sep 1, the balance will go back to zero in that account.

To correct your issue now, create the account as a bank account, post an entry like the second one I mentioned (debit the clearing account, credit the bank) in the general journal on Aug 29.  This will allow you to clear the withdrawal for payroll on your Aug bank statement.

Then on Sep 1, post another general journal entry that will debit the bank and credit the clearing account.  In your Sep bank rec, you will see sum of the individual cheques already posted (Withdrawal side) will match with the amount posted in this general journal entry (Deposit side), so everything will balance.

Hope this helps