In one exchange, you'll be able to make a MIS buy order, while in the other, you'll be able to put a MIS short order. Both of these trades, however, must be squared off individually on each exchange before the end of the trading day.

If you own shares of a firm that trades on both markets, you can sell them on one and then buy them back on the other. Even if these trades are classified as CNC, all fees, including the STT, will be applied as if they were intraday trading.