If you fly Bali/Jakarta/Sorong on one ticket, I think your bag will go with you. It's always good to check the bag tag and see what it says. Also, asking at ticket pickup to clarify, if they can understand you.
The other thing that nobody has mentioned with Garuda vs all the other airlines... Garuda gives you 40kg of baggage if you say you have dive gear. The other airlines make you pay, and I just paid $200ish for my 21 kg of overage. So the flight ended up costing me $400 one way (but Garuda didn't fly the route I needed.)
I am a big fan of Garuda because it is as reliable as they can be. Best airline in Indonesia, IMO. They also serve food on all the flights I've been on with them. They also are Sky Team, which I have Platinum/Elite status and their associated airlines tend to be good quality.
I've flown the 12:30AM flight from Jakarta to Sorong 3 times so far, it's been on time, baggage arrived happily. I just got back from Indonesia today, and flew Maumere (Lion) -> Kupang (Lion) -> Surabaya (Lion) -> Jakarta (Garuda, had to get my bags, convey them to the international terminal and check in with new airline) -> Incehon (Delta/Korean Air) -> Detroit (Delta, had to get my bags to go through customs, really obvious because everyone is doing it -> Chicago. Delays on Lion air flight of 2 hours that made me worried that I would miss my connection in Jakarta, but I made it with an hour and a half to spare.