You will have to deal with Qatar Airways Holidays for any upgrade related queries. Just like BA Holidays bookings, I suspect the "normal" QR customer service line would probably not be able to service your booking and rather direct you to contact the Qatar Airways Holidays phone line (if they have one) or email.
This isn't uncommon for package holiday bookings to have substantial discounts/benefits like this. It is quite frequently seem on BA Holidays as well where sometimes just adding a car for one night can subsidise the flight cost quite a bit. The final price you see prior to payment will be what you pay to QR Holidays. It is worth reading the fine print to ensure the hotel doesn't charge any extra local resort fees or taxes or whatever. This should usually be mentioned somewhere along the booking pathway.
You may find these FAQs helpful:
https://holidays.qatarairways.com/en...S¤cy=USD