When you use direct deposit for your payroll check your funds should be availible at midnight the day of the deposit. EFt's are different than a check, the convience of DD is so that you have your funds availible faster and without having to go to the bank or Credit Union.
You can go to a personal banker and have your overdraft charges reversed if the sutuation is the fault of the financial institution, however if it is the fault of your employer and they wont cover the charges the bank can only undo so many nsf charges so you may not be able to get all of your $ refunded
I hope you can get this straightened out and if your employer knew that your check would be held up or late then they should have sent a heads up!
best of luck