I am quite confused

Do we have to put the number of master cartons we are sending to the Amazon warehouse here or the number of boxes the customer will receive when they place the order?

Please Help.

This is the number of cartons you will be sending to Amazon FBA.

As @FunkyMonkey says. But it could be the number of boxes that the customer will receive for the product. Ensure to properly label each unit with FNSKU barcode.