Vat calculation for online

Hi Friends, 

I need to know that we are selling our products online and on our behalf online portal is creating invoices inclusive of VAT 5%. 

For eg: Our Product is Priced with 5% Vat as 699/- (at which invoice is generated) and now the portal is paying us after deducting 12% commission of the website + Courier Charges + Handling Charges. At net we are paid with Rs 542/-. I need to understand that do we need to pay the VAT on 699/- or 542/- and secondly what entry will be shown in Tally or Quick Books. I use both the softwares for making our accounts. 

Your reply and guidness will be appreciated.

Thanks

Sumeet