Hi there, @Tdub.
Welcome to the Community. I can share some insights about the merging process in QuickBooks Desktop.
You can use the Intuit Interchange Format (.IIF) tool in importing your lists and transactions in QuickBooks. However, payroll transactions need to be manually entered in QuickBooks Desktop.
There are 2 ways in entering your year-to-date amounts, either inside or outside of the Payroll Setup window. For more details, you can refer to this article: Enter historical payroll data in QuickBooks Desktop Payroll.
I also recommend getting in touch with your accountant to verify if they have the QuickBooks Desktop After-the-fact payroll. This allows them to efficiently enter, verify and adjust paychecks all from a single spreadsheet-style screen.
That should help you merge your accounts, @Tdub. Let me know if there's anything else you need or if you have follow up questions. Have a good one!