Where will you pick up/leave the Seven Seas boat from?
You can get domestic flights from Sorong or Bali to the Manado area, there is great diving there and resort based budget room accommodation (room and board for US$25 or less, rates for longer stays are negotiable in the smaller places) is available at many good places near Manado.
I recommend both Bunaken Island area,(wall diving) as well as Lembeh Straits area (great muck diving and night diving)
The people in that part of North Sulawesi are terrific, very friendly, always singing and laughing. See the other discussions for details .
Be sure to apply in advance at an Indonesia Embassy or Consulate to get the 60 day visa. You need to check in your country on the availability of that visa and any other regulations related to the country for which you have a passport for. . Normal visa on arrival is only 30 days (available for US, Canada, Most of Europe etc) (US$25 in US$ cash) and can not be renewed in country.
Some people do a visa "run" to Singapore or the Philippines, but that involves extra time and the expense of the flight etc.
Since you have plenty of time and flexibility, it will be easy to get domestic flights. Perhaps your dive operator can help you make the arrangements as it is difficult to book domestic flights from abroad and if fly Garuda domestic flight and book way in advance from abroad you will likely pay way way too much money. typically their prices will come down as it gets closer to the departure date and they see what others are charging.
Also Indonesia is very strict about the fact that you must have at least six months of validity left on your passport when you arrive!!!!
Restaurant (or dive resort food, usually include with accommodation) Food is pretty inexpensive so that there would be no reason to do your own cooking. And you don't want to be in a big city, they are crowded and hot. You want to be near the ocean or in a nice place in the mountains
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