Hi HR -
You will certainly love Raja Ampat and the ability to get to all of the best dive sites on a liveaboard, the best way there is to dive til you drop.
Though most who have been on liveaboards will say that there is never a problem with skeets out on the water, if you are in a quiet anchorage near shore it can be different. Malaria meds will give you peace of mind ... many threads on SB about taking them. There are several ... forget which one is recommended for that area.
My personal guideline for Nitrox is ... 4 dives a day, 60-70 min, air is OK. 5 dives, time to go to Nitrox, at least on some dives. YMMV. If you get your EAN cert, you at least have the flexibility.
Don't know if you have your air already booked, but we like to stay in Bali for at least 3 days before shuttling to the boat, so we're rested and past jet lag. It makes the start of your diving more relaxed and probably safer.
Ubud is the cultural capital of Bali, about a 1.5 hr taxi ride north of the airport. Accommodations for any/every budget and style of travel. Good food in town, markets, local dancing, etc. Take a 5 min walk out of town in any direction, and you're in the silence of rice fields.
Forget travelers checks ... hard to use there. Take credit card(s) and new, unmarked US bills, preferably $100's, and change them for rupiah (IDR). Everywhere on the street people will have their exchange rate posted, so you can shop for the best one. You will use rupiah more than credit cards, except for larger retaurants and hotels. Check ahead to see if the Dancer will take a credit card for your on board extras.
As long as you're not walking around on the back streets of a big city at night, Indonesia, at least the parts you're visiting, is pretty safe. Bali even more so. The Balinese are the nicest people in the world, IMHO, especially if you get a few minutes outside the heavily commercial tourist areas.
PM me if you have any more questions, and have fun. We'll be back in Indo in October for a Komodo liveaboard ... can't wait!