You must account to the VAT Authorities for all VAT charged to customers and paid by you on purchases of goods and services.
You must account to the Federal and State Tax Authorities for all Sales Taxes charged to customers.
You will need to set up a VAT / Sales Tax Collected account for each relevant Tax Authority in the Current Liabilities section of the Account Names list. These are used to accumulate all the automatically calculated VAT / Sales Tax amounts of the transactions you enter.
Next you will need to set up a parallel Tax Authority accounts in the Current Liabilities section of the Account Names list. Thes are used to record the amounts you have declared and paid to (or received from) the Tax Authorities.
Next using Menu|Lists|Value Added Tax, you should define the VAT / Sales Tax rates you will need to account for. These will be the different rates of VAT / Sales Taxes you are likely to encounter in your business transactions. For the purpose of preparing VAT Returns, I strongly advise you set up different rates for Sales and Purchases and for European Sales and Purchases if relevant.
When entering individual transactions, you should select the relevant tax rate where appropriate. The system will accumulate the correct tax for each item in the Tax Collected account you have specified. The Net of Tax amount is posted to the Goes To reference you select at the time of entering the transaction. The Gross amount is shown in the account in which you enter the transaction eg, a customer account.
When you need to make a Tax Return, click the 
button in the main toolbar in order to display all your VAT transactions.
The tabs show all the tax rates you have set up and all the transactions for each rate.
These controls allow you to flip the transaction amounts between the Gross value, Net of Tax and Tax amounts.
These controls allow you select the Tax reporting period.
Using these facilities you can quickly fill in your VAT / Sales Tax return for the period.
Next check the Tax Collected account to see if the balance at the period end is the same as the figure you have calculated. It may be that you made some valid accounting adjustments for the preceding period which changed tax values previously reported. You will need to adjust your tax return to take account of any such changes.
Next make an entry which transfers the tax amount owing as reported on your current Tax Return from Tax Collected to the Tax Authority account. When you make your payment to the Tax Authority, the balance on the account will go to zero.