There are direct flights to Ambon from Jakarta, Surabaya and Makassar as well as from small airports in Maluku and West Papua. Garuda and Lion Air fly twice a day from Jakarta to Ambon. From Bali, Garuda and Lion Air fly to Makassar, with onward flights from there from Sriwijaya and Lion.
Jakarta airport has a free shuttle bus between the international and domestic terminals until 11 pm, taking up to 30 minutes. After that a taxi can take you between the terminals. If you need to wait for some time at the international terminal, Saphire D´consulate Lounge provides armchairs, sofas, WIFI, showers, food, coffee for 180,000 IDR p.p.
Indonesian domestic flights are often delayed, so please plan enough time for your travel and connections. Some airlines give only 15 kg free luggage but overweight luggage is generally charged at only 10.000-17.000 IDR per kg. If you mention with a friendly smile that you have dive gear, you may be able to check in overweight luggage without extra charge. Tall passengers should try to book a seat in the emergency exit row. Indonesian domestic airports charge a departure fee (none for transit).