If your supply is designed goods and your turnover is Rs 5 lakh you must register. (This is wrong. designed or undesigned goods, you have to register if your turnover is above Rs 2 lakh.)
VAT returns are filed every month or every quarter... VAT return is to be filed every quarter. (All VAT registered dealers are required to file monthly returns except those registered under the Composition Scheme.)
Subtracting input tax ...is at the discretion of VAT officer (There is no question of discretion. The concept of VAT itself is that you have to deduct input tax from output tax and pay the difference.)
In certain case, comissioner may pay you excess (Excess tax paid and refundable should be carried over to the next tax period (ie. till the end of the year and only after the last return of the year is filed, the excess will be paid back. However, only in the case of exporters, the excess is paid back after the monthly return is filed.)