If I buy 50 shares of Glenmark @ 800 and 50 shares @ 790, brokerage charges will apply (20+20), or 20 rupees. A single script is traded, but different orders will be placed?

Zerodha charges Rs 0 for equity delivery brokerage. You don't have to pay anything.

Intraday brokerage charges for each'successfully executed' order.

If both transactions are part 1 of the order, then you will only pay Rs 20. It doesn't really matter how many transactions you order in exchange.

If they are part a different order, separate brokerage charges of Rs 20 per order will be charged.