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Hi,
I am by no means an accountant so please bear with me as this may be a really stupid question.

My last BAS was the first time I reported on PAYG, let's say a value of $x for quarter 2. I obviously paid that amount to the ATO when I submitted the BAS during quarter 3. During quarter 3, I withheld $y of PAYG. Now, when doing my BAS for quarter 3, the PAYG withheld amount that appears on my BAS to submit is $y-$x instead of $y. Is this correct? Should it be reporting the amount withheld minus any payments to ATO instead of the entire amount withheld during that period?

I can understand if from an accounting point of view it is correct but at the same time I am worried that I may be reporting the incorrect amount.
 
I am using quickbooks plus 2008/09 R8.

Thanks

I'm not an accountant, either, and I find each BAS gets harder than the last. An accountant who know QuickBooks well recently came to assist me with my books. She suggested not using the QB BAS reports, because on mine, certainly, they were not accurate and threw up more problems than I started with. She suggested printing up the following reports:
Tax Summary Report
Payroll Summary
Use the figures from Tax Summary and fill in on the GST calculation sheet from the ATO. Remember to add back the GST onto the figures which are net (no GST included), because the ATO treats the figures as including GST.
The Payroll Summary should give you the amounts withheld in PAYG to put on your BAS.

Just a warning too: I have had problems in the past when I have paid the money owing on BAS and recorded it as Tax Payable, because QB does not allow splitting the tax liability cheque into tax payable and payroll liabilities (PAYG). I have had to create a journal entry crediting Tax Payable and debiting Payroll liabilities: PAYG to separate the amount paid in PAYG from the total cheque paid to the ATO.

The PAYG reported on your quarterly BAS should only represent what you have withheld since your last BAS.

Provided that you have the correct tax codes assigned and you are recording payrolls correctly QB should do it automatically for you quite fine.

I have a very good understanding of my business and know what figures should look like, and can usually spot an abnormality right away.

you will develop this to as you progress i was nervous the first couple of BAS i did. but can now do my quarterly BAS in less than 3 mins.

a good practice is to use the working sheet they give you with the BAS using figures from your tax summery and payroll summary double check your work and then run the auto BAS in QB when you have a good grasp on how it works and how to spot a mistake you wont need to do it manually

I do many bas statements per month and quarterly and the one thing I do advise clients to do is check the PAYG figure from your payroll report with the PAYG amount appearing as a liability on your balance sheet.  So you should run a balance sheet for the date at the end of the quarter or month (if you pay monthly)and reconcile the amount appearing in this report with your Payroll report.  It does depend, however, on whether you just have one account for payroll liabilities which would then include your superannuation liability as well.  You should have one account for PAYG withholding and one for superannuation liability and when setting up your payroll item lists you post the PAYG and Super to the correct accounts as the default is payroll liabilities.
I have seen many accountants spending hours reconciling these accounts and this costs you money!