I had this same issue and struggled for months with frustration. I changed bank accounts and my payroll accounting was coming from my old account but the money was coming out of the new account causing an imbalance in my QB accounting.  I recently learned how to fix it! Go to gear icon, payroll settings, Account - way at the bottom, change your bank account from there to your new one.  Going forward your payroll should always pull from your new account.  I had to do one big journal entry for the dollar amount that was wrong to fix the internal QB accounting.  I hope this helps some of you as I struggled with you too!