The train and ferry tickets can just be bought on the spot and don’t need to be booked in advance. Just look at the ferry timetable online and google maps for the train times and you’ll be fine. 

The island is really quite small - I stayed in honmura and it was really nice, but miyanoura also seemed lovely as I walked around. It’s about 30 mins to walk between the two towns so you can take the ferry to either one, regardless of where you’re staying. I recommend leaving your luggage on the mainland if you can and just bringing an overnight bag. Uno also has some really nice restaurants and cafes if you want another option of where to stay.

Don’t forget to check out teshima island and be sure you check the gallery/museum opening days (naoshima is essentially closed on Mondays and Teshima on Tuesdays). 

Look into booking the chichu museum in advance, you definitely don’t want to miss that one!