In Manado or even in Sorong, you can get pump spray type called "AUTAN", as shown above. I bought one from one of the local convenience store in Sorong within walking distance from SwissBelHotel.
On another occasion, I just walked across the street from the hotel & talked to a motor bike taxi guy (the local called it "Ojek") to take me to a pharmacy (called "Apotek") to get me another medicine. I just hoped on to the back of his motor bike had a little 10-minute tour around the town to the pharmacy, bought the medicine, hoped back to his motor bike, he took me back to the hotel, paid him Rp.15,000,- (about $1) for the 30 minute joy ride around Sorong
I took malaria med for my first trip to Raja Ampat, back in 2010, but didn't like the side effect of it. On my 2nd to 5th trip, including a trip to Manokwari to liveaboard dive with whalesharks in Cendrawasih Bay, I didn't take the malaria medicine any more and I'm still free of malaria (knock on wood).
The main thing you need to do to protect from mosquitoe bite is to apply the Autan spray on your exposed skin, while you are on the harbor, waiting a ride to the liveaboard or to the resort. That's all. No malaria on the liveaboard, nor on the resorts that I've been to, leaving from Sorong harbor (4 liveaboards, 3 resorts).