Depends on your broker. Generally same funds can be used for EQ/FNO/CDS however for MCX funds need to be kept seperate. Simply because MCX has a different regulator and they don’t seem to have come to terms with SEBI on this. However there are a few brokers that allow you to use the same funds for all segments including MCX. But as it is restricted most of the reputed brokers do not allow clients to use same funds in MCX and other segments.
For MCX commodity trading (if you want to use the cash in your EQ trading account), you need to withdraw your funds from EQ to your bank account and transfer again to your MCX trading account. This will take one day.
No, it is separate in Zerodha, Equity A/c is separate from Commodity A/c. You need to withdraw it firat from Equity A/c and then transfer it to Coommodity A/c and vice versa.
Check this blogpost on why you can’t use the same funds for equity and commodity: http://insiderview.comparebrokerages.in/can-i-transfer-money-between-equity-and-commodity-account/