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If there's no customers assigned to employees, you can track their time without a customer attached to your records. In the event there's any amount of customers assigned to an employee, they'll need to choose one when clocking in.
Your Customers & sub-customers option in QuickBooks Online Integration Preferences refers to whether you're syncing new customers to your books or not. If you have it unchecked, new customers you create won't be synced into QuickBooks Time.
You'll also be able to find many detailed resources about using QuickBooks Time in our help article archives.
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