If you do not use KeyPay to process your payroll, you can input your W1 and W2 amounts directly in the BAS report screen within Quickbooks.
If you process pay runs through KeyPay, W1 and W2 line amounts in the BAS report are determined from the journal entries created automatically in QuickBooks from KeyPay.
If you look at a journal entry posted from KeyPay, you will notice that certain lines of the journal entry will have a GST code applied: BAS-W1 (Purchases) and BAS-W2 (Purchases). These tags are used by QuickBooks (along with the date of the journal entry) to determine the W1 and W2 line amounts that show on the BAS report. These Tax rates are created automatically the first time a payrun is created in KeyPay and pushed to QuickBooks.
W1 line amounts are typically applied against the full wage expense incurred by the pay run, and will have a GST code of BAS-W1 (Purchases).
W2 line amounts are typically applied against a PAYG Withholdings Payable account for the amount of PAYG withholdings made by the payer that then needs to be paid out to the ATO later, and will have a GST code of BAS-W2 (Purchases).
If the amounts on your report are different than what you expect, the first thing to check would be that all of the pay run journals to make sure that the dates and amounts are correct, as well as the correct GST code applied.
If the values in the journal are different or incorrect, you can go back to KeyPay, undo the payrun and re-finalise to pass the journal back into QuickBooks once more.