How do a reflect a manual check given to an employee on July 1 that was not run through QB on this check?

I've got some steps to handle your previous paycheck that wasn't run through QuickBooks Online, cjlandstrom.

You can create a journal entry to record manual payroll. But before proceeding with the steps, I suggest consulting with your accountant for guidance on which account receives the debit and credit side of the transaction. This is to ensure the accuracy of your books.

You can follow through this article the detailed steps on manually entering payroll checks in QBO: Manually enter payroll paychecks in QuickBooks Online.

If you need help with other tasks in QBO, you can browse for specific topics and look for responses that fit your concern on the QuickBooks Help page.

The Community is always open to help you again if you have any other concerns or follow-up questions about processing payroll in QBO.