Both destinations are served by Goa (GOI). Since there's no flight route between them, the best way to travel is by road.
South Goa
Fly to Goa (GOI), then travel by road to South Goa. Taxis, buses, and private cabs are available from the airport.
Alnavar
Fly to Goa (GOI), then travel by road to Alnavar. Local transport options include taxis, auto-rickshaws, and state buses.