Q: Can I make changes to the employee's QTD/YTD Totals? How does this affect the W-2's?

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A: The QTD/YTD Totals gets its information from the individual paychecks.  Every time a check is created, this tab is updated - creating the appropriate lines based on the Master Paycheck (Fig 1).  Also, the Test Totals process found on the Quarterly Processes can recalculate the QTD/YTD Totals based on the paychecks.

(Fig 1) Master Paycheck Screen

Changes made to the QTD/YTD Totals should also be made to the Master Paycheck, so that future paychecks update the totals properly.

The W-2 Totals tab gets its information from the QTD/YTD (Fig. 2) Totals.

(Fig 2) QTD/YTD Screen

Therefore, any changes to the QTD/YTD Totals will be reflected on the W-2's. 

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