Welcome to the Community, @RKX.

Allow me to share an idea about importing data to the QuickBooks Online account.

To avoid duplication of transactions, you can delete the manually imported ones. It is to ensure that all the transactions imported are not yet in the account. That is for the transactions you imported that are the same as the ones you are importing.

Additionally, here is an article you can check to process historical payroll: Set up a prior payroll for QuickBooks Online Payroll.

Keep me posted if there are other payroll questions you have. I'll be right here to keep an eye on your response. Take care!