What shailesh has said is absolutely correct. All your queries should get satisfied with that.
Still i am explaining to your latest query.
As Shailesh said that the CST A/c and VAT A/c shall be opened under Current Liabilities. This means that VAT and CST shall not form part of the Profit and Loss Account but Balance Sheet. In case of CST paid on purchases, it is no doubt included in cost of purchases. In case of VAT that is eligible for set-off and VAT on Sales and also CST on sales, these will not form part of Cost of Goods sold and Sales Turnover.. These will form part of Current Liabilities, if net VAT is payable and will be transfered to Current Assets if net VAT is refundable.
Morever, in addition of your query, i will also let you know the impact on the inventory.
According to AS-2 on valuation of inventory, the Closing Inventory shall be valued net of the Duties and Taxes paid to Revenue authorities on purchases that are eligible for regund or set-off. So while valuing Inventory also, all the refundable duties and taxes shall not be included in the Value of Closing Inventory.