A direct deposit deadline means that you have to submit your direct deposit payroll two days before the pay date, regardless of the pay period. For example, if your pay date falls on Monday and you submitted your direct deposit payroll the same day, it'll be posted on your employee's bank account on that Wednesday.
If you missed the direct deposit deadline, but it's still before the pay date, you can create a paper check for the employee. I've included the steps below to do this.
On the Workers tab and Employee section, click Run Payroll.
Next to the employee name select, Create another check for [name].
Enter the payroll information and process it as you usually would from there.
Please note: Make sure to select Paper check before you run the payroll.
For future references, I've included a couple of articles that go into further details about deadlines.