Fly from Jakarta to Pangkalan Bun. Pre-arrange with a local tour operator to access Tanjung Puting NP by Klotok boat. Avoid high season for best experience with less tourists.
Fly from Jakarta to Labuan Bajo on Flores. From there access Komodo NP by boat. Pre-arrange with a travel agent or hotel.
Easiest way to get around on Flores is by scooter. Fuel is sold in bottles at roadside “Kiosks”