QB Issue Resolution:

You can definitely do that!

You’ll need to select Run Payroll and then unselect all the employees who will be paid later with a check. You’ll then process payroll as you always do. This will submit the payroll for the direct deposit employees only. Then on the regular pay date you’ll select Run Payroll and unselect all employees who were paid by direct deposit and run payroll as usual. This is all you’ll have to do to run the separate payrolls.

Resolution for Issue 'Not all my employees are set up on direct deposit.' available: Yes (Solved).
Source: Intuit Community forum.

Not all my employees are set up on direct deposit.: this issue or error code is a known issue in Quickbooks Online (QBO) and/or Quickbooks. Support for this issue is available either by self-service or paid support options. Experts are available to resolve your Quickbooks issue to ensure minimal downtime and continue running your business. First try to resolve the issue yourself by looking for a resolution described below. If it is a complex issue or you are unable to solve the issue, you may contact us by clicking here or by using other support options.

Support for Direct Deposit
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Error Recovery for Direct Deposit [Canada]
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