I ran payroll using Check option since the Direct Deposit was above limit. How would the check be processed by Quickbooks? Should I write, and process check manually?

Let me help you create a manual paycheck in QuickBooks Online (QBO), aaron58.

We can set the Pay Method to Paper check for you to process a manual paycheck to your employees. Let me show you how: 

1. Go to Payroll on the left side menu.
2. Choose Employees and click Run Payroll.
3. Select the name of the employee.
4. Make sure that the Pay Method is set to Paper check.
5. Enter all the payroll details and tap Preview Payroll.
6. Press Submit payroll.
7. If the employee has already been paid, just click Finish Payroll instead of Print paychecks.

You'll want to run a couple of payroll reports after running payroll. This helps you review the amounts of the paychecks and liabilities to make sure that everything is accurate and good to go.

Feel free to browse this link here if you need help with other tasks in QuickBooks Online Payroll. It'll route you to our general payroll topics with articles.

Drop a comment below if you have follow-up questions or concerns creating paychecks. I'm more than happy to assist you. Take care always. 

I have already run the payroll with the Check method. But, how do I pay the employee? No funds have been transferred to employee's personal account from the Business Account? How does the employee get paid actually? Who will write the physical check for those wages and who will deposit wages in employee's account?   

I appreciate you getting back to us, rnj-consulting-o.

Since you chose a paper check in paying your employees, the fund will not be funded to their business account. They need to en-cash the paper check you've printed.

To know more other ways of paying your employees, check out these articles:

Turn off direct deposit for an employee.

Ways to pay employees.

I'll be right here if you have any other concerns. I'd be more than willing to lend you a hand.

Thank you, Rose. I don't think what I printed out of the Quickbooks Payroll will be accepted by the Bank. But I can try going to the Bank. Also, if I understand you correctly, I have to write a physical check and give it to the employee to cash it?

It's nice to have you in the Community, @rnj-consulting-o. I'll take care of this query about the payment method for your employee.

Yes, I agree with @Rose-A that you'll need to write a paper check for encashment as the payment method to your employee.

Also. I’ll be adding this handy article for more details about the payment method for employees or contractors.

In case you'll need helpful links and guides to assist you in doing QuickBooks Payroll tasks, you can visit our QuickBooks Help Page. From there, you'll find a number of help articles and even video tutorials based on what you've searched. You can also bookmark them in your browser for easy access and use them as your future reference.

I’m always ready to assist you if you have any other questions or concerns about managing your payroll. Tag me in your reply and I’ll sprint back into action. Have a good one and keep safe.

Thank you, Carneil. 

It seems I had to order Checks through Quickbooks, which is another lengthy process. Or I can do this entirely manually now. 

I wish this was known to me rather than struggling for last 5 business days and not having access to funds.

This was a huge learning for me hitting the Direct Deposit limit, not understanding what the limit is, and how to process manual checks. 

I would recommend that someone should update help section with proper guidance.