Mvat return and audit

a motor bike agency has done MVAT registration .The business was started in june 2012.VAT is paid to the motor company every time the client buys stock from Company. he has not paid any VAT since the INPUT VAT is higher than the VAT payable.He has not filed any return due to unawareness of the same. he wishes to comply with VAT provisions and file return. how to file return what are the penalties for late filing? by which date he has to file return? return should be filed online or physically? does he have to get statutory as well as VAT audit done.His turnover has crossed 1 crore.