Welcome to the final step of your integration setup: the Deduction Audit. You're one step away from going Live — where new enrollments, life events, Open Enrollment, terminated benefits, and other events causing per pay cost amount changes will flow in real-time.
This guide walks you through three simple steps:
- Pull your deduction data from Payroll for comparison
- Reconcile any code mismatches and amount discrepancies
- Notify your EN Payroll Analyst to flip you fully Live
How the Deduction Audit works
The Deduction Audit pulls in your payroll deductions (and employer contributions, if available) from your partner's system so you can compare them with Employee Navigator's data and fix any differences. Once all values match for each employee, you can go fully live—after that, changes sync automatically to payroll in real time.
The audit groups discrepancies into four buckets so you can quickly focus on what needs attention.
Here's an example of what you'll see (after you've imported your deduction data) when you open the audit from your Payroll tab → Continue Setup → Deduction Audit → View Audit:
What each section means & what to do:
- Codes that exist in one system but not the other
- Left side: codes mapped into EN but not found in your Payroll system's data returned to us
- Right side: codes returned from Payroll but not in EN — typically 401k, garnishments, etc. that aren't part of the integration
- Per-employee deduction differences shown side-by-side
- Statuses: Not in EN, Not in Payroll, Amount Discrepancy, Employee Not Synced
- Resolve with Send (push EN → Payroll) or fix the underlying cause in EN if payroll's amount happens to be correct. For most partners, you can also resolve with End (push EN → Payroll) to stop deductions in payroll.
- Deductions matching exactly between EN and Payroll
- Already-synced deductions land here on import
- When you Send a discrepancy, it moves here automatically
- Codes you've marked as outside the integration's scope
- Common examples: 401k, garnishments, child support
Who's your payroll partner?
Pick your partner so we can tailor the demo to your import method. The audit screens look identical for both methods — but you'll start them differently.
Pull your "EN Deduction Report" from your payroll system, then import the file into Employee Navigator. The flow is the same after — scroll down to launch the demo →
Walk through your audit — start to finish
Click into each section, resolve real code and amount discrepancies, and watch your deductions flow between Employee Navigator and your payroll partner in real-time. Every button works.
FAQs
QI have employees who must receive post-tax deductions. How do I configure this?›
If they are not 2% shareholders: Create a new Payroll Group with the same frequency, add the post-tax deduction codes to that group along with any other pre-tax codes for plans that must be withheld pre-tax for everyone, then move each applicable employee into the new group.
If they are 2% shareholders: Go to their Profile → Employment → Statutory Class → choose 2% Shareholder and Save. EN will then apply only the post-tax deduction codes you've mapped into your Payroll Group(s) for that employee.
QCompany owners or executives don't pay for benefits. How should we handle that?›
Work with your broker to set up a benefit class where benefits are 100% company-paid, so EN reflects $0 cost for that segment of employees.
QWhat if the deduction amount in Payroll is correct, but EN is wrong?›
EN is the system of record for deduction amounts — we'll never pull a value from Payroll. So a manual adjustment in EN is required.
Contact your broker, since an incorrect EN amount usually points to incorrect plan rates, the wrong coverage level, or rate changes that haven't been applied. Once corrected in EN, sync the new value to Payroll and it'll replace the previous deduction amount.
QIf an employee has both Annual Salary and Annual Benefit Salary, which one drives benefit calculations?›
Annual Benefit Salary always wins. EN uses that value whenever it's populated.
QWill future-dated deductions in my audit be sent automatically once the integration is live, or should I push them myself?›
No. Future-dated deductions need to be sent manually during the Deduction Audit using Send to Payroll. They'll send with the future effective date so employees aren't deducted before their start date.
QMulti-EIN companies — anything different?›
Pull and finish one Deduction Audit at a time before moving on to the next Subscriber Group. Best practice is one-at-a-time, fully completed.
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