Regardless of the time of day you decide to fly, the ticket price will remain around the same. Book flights from Jakarta to Cusco as you normally would.
If you book a flight to Cusco from Jakarta, you will be flying to Velazco Astete, which is the city’s only airport. Cusco Velazco Astete (CUZ) is located 2.7 km from the centre of Cusco. There are 0 flights from Jakarta to Velazco Astete per day from 0 different airlines.
These are just IATA (International Air Transport Association) codes. They are used in aviation to identify and differentiate airports. That’s why a Jakarta Soekarno-Hatta Intl Airport to Cusco Velazco Astete Airport flight would often be abbreviated as a CGK to CUZ flight.