Entered my payroll. Hit 'export'. All checks show as exported, but only 3 exported to my desktop. I imported that iif file and it was only 3 paychecks.

Good evening, @wendy94. 

Welcome to the Community! Let's work together to get these checks exported from QuickBooks Online to Desktop. 

Before digging further, can I have some more details and screenshots of the issue? 

I want to be able to determine the best solution for your business. In the meantime, here's a guide that can provide some additional information: 

Export your payroll data into QuickBooks

I'll be waiting for your response!