You have a separate NSE (includes NSE, BSE and CDS) client account and MCX client account.
You will have 2 ledgers on the trading platform, equity and commodity.
When you want to transfer funds from one ledger to other, you will have to go put a request to do the same on backoffice.. while opening the commodity account, you would have given us an authorization to move funds from your commodity ledger to equity ledger and vice versa.
We will transfer money on your behalf, but for the intermediate time when the transfer is happening we will give you credit from our deposits with the exchange for no additional cost..