Once hours have been submitted early, you will need to manually create and run an off cycle to accommodate for any unpaid hours for the remainder of the pay period. This is why the user must acknowledge the limitations of the early submission. We are working to automate this, however, for the time being, it is a manual process.
Zenefits will create a task in the Payroll Overview page to remind you of any unpaid hours. However, the remainder of your workers' hours will not automatically submit to payroll. Workers can continue to clock hours, and these hours will auto approve at the approval deadline. Then, you may download the hours and upload them into payroll using the Bulk Earnings upload.
Alternatively, you may also wish to approve the entire pay period at once, and not have to worry about running an off cycle for any remaining hours. In order to go this route, the administrator would need to project the remaining hours for their workers and submit the timesheets early. They can use the next scheduled pay run to make any adjustments to their workers' actual hours.