Outside Payroll Service and QuickBooks Integration
Most payroll services now have a QuickBooks import routine available. Based on a limitation of the SDK, developers do not have access to the payroll related activities. For this reason, depending on the service used, the payroll will either be imported as checks or as journal entries (i.e. not as paychecks or payroll liability checks).
Based on my experience with Paycheck and ADP specifically, the integration process works best when using account numbers in QuickBooks. The next challenge is that the set up screens typically have any option available, even if the payroll does not use those deductions or taxes. Each choice in the payroll service set up screen needs to have an account number assigned. This is the "mapping" that converts the payroll register information into the entries for QuickBooks. This set up process is critical to correctly reflect the gross wages, payroll tax expense, payroll liabilities, etc. as needed for financial analysis purposes. Most clients will need the help of a professional at this point to confirm everything has been set up properly. Once the account numbers have been entered and saved, create a test file from the payroll service for the last payroll.
Confirm no one will be using the QuickBooks data file during the testing process. Back up the QuickBooks file and then try to import the file. Look immediately at the results and reconcile all the totals between QuickBooks and the payroll reports. If there are any errors, restore the QuickBooks back up file, make the corrections, export a new test file, import it, and reconcile. Continue this process until all the information is being imported as desired.
Although time consuming to set up and test initially, it saves countless hours from re-keying in the long run.
More information on this topic
Outside Payroll Service
State Payroll Tax Returns