From the west coast, I've flown Singapore Air through Singapore a couple times. Not the cheapest, but Singapore's a great airline and Changi is the airport to which all others aspire IMHO. Don't know about other embarkation cities, but the flight from LAX gets you to Singapore around 1 a.m., then you check into the transit hotel right in the airport (there's one in each of the 3 terminals) for a nice nap in a real bed and a shower before continuing on to Manado on Singapore's regional carrier, Silk Air, in the mid morning (9:30-10:30 as I recall). Super easy and recommended.
On the other hand, getting to Sorong is an adventure. I have heard the flight from Manado to Sorong is problematic with cancellations, luggage delays, etc. I've never done it, so consult others with actual experience. When I flew to Sorong last fall, I was encouraged and so went through Jakarta on Cathay instead (lots of airlines can get you there). This requires an overnight in Jakarta as the best outbound to Sorong leaves very early in the a.m. and goes via Makassar (Ujang Pandang), getting you into Sorong in the early afternoon if all goes well. You can also go through Bali, which is always great, esp if you can spend a few days there on either end. I think then getting to Sorong requires another overnight in Makassar.
What ever way you go, I'm told it's best to get your intra-Indonesia ticket from a local agent in case there are problems. All the local carriers change times, combine and/or cancel flights at their whim, so keep checking on them up until the time you actually get on the plane.
You will have a great trip!
Phil