I am running payroll for first time after converting from Quickbooks Desktop but pay details end up as journal entries in register. How do i pay employees by cheque.

A jolly good day to you, jwrcatreasurer. 

You'll want to sign up for a payroll plan in QuickBooks Online and complete the setup first. Here's how: 

1. Go to the Employees tab. 
2. Click the Choose my plan button, then select a plan that works best for you. 
3. Follow the on-screen prompts to set up your payroll service.

Before running payroll, you'll want to check for any missing payroll details and year-to-date amounts. We recommend looking at the payroll reports in QuickBooks Desktop.

After reviewing the data, you're ready to pay your employees. 

When converting to QuickBooks Desktop, some payroll transactions that affect accounts are converted to journal entries. These are usually liability refunds, adjustment, and opening balance transactions.

More details can be found here: What to expect when you switch from QuickBooks Desktop to QuickBooks Online.

Just expand the Payroll and Payroll items links. 

This article is also handy if you need help with other tasks after the conversion: What to do after converting from QuickBooks Desktop for Windows or Mac to QuickBooks Online.

You can also check our Payroll articles page for a list of payroll topics. 

I'm pretty sure your employees are going to be happy with their pay. Please let me know if there's anything else I can do for you.