These days most of the operators seem to be arranging connections to Sorong through Makassar (Ujung Pandang) on Pelita. There also is (or was) the direct flight on LionAir from Manado to Sorong, but it might not be every day. But I've been told this connection is considered less reliable than the Makassar flight on Pelita.
I'm sure that Tony Rhodes and the Kararu people will be able to figure out the best routing for you from Manado to Sorong. Follow their advice. If they say that it's best to fly back to Makkasar and then on to Sorong instead of taking the shorter, direct flight on LionAir (if that flight is still happening), I'm sure there's a good reason.
I just did the flights from here (Bali) to Sorong and back (via Makassar) a few weeks ago. We had to overnight in Makassar on the way out, but the people organizing our trip still didn't want to risk to Manado connection. Our group pooled our check-in bags, so there were no over-weight charges on either leg either way. I was carrying both a Pelican case with housing + ports and Phototrekker backpack with cameras and lenses as carry-ons. I was allowed to carry on both after explaining that these were sensitive photographic gear. The overhead racks in the Merpati and Pelita planes (Fokker something-or-others) are not big enough for either of these, but I was allowed to stow both in a small locker area in the rear of the plane, and was not required to check them.
In the past, some people have had problems of checked-in bags (with all clothes and all dive gear) not arriving in Sorong with them, and only following several days later. Everyone on one boat ended up diving with gear cobbled together from the spare bits on several boats and wearing the same swim suits and T-shirts for 14 days.
I'm not aware of this happening this season, but it did happen last year. It's probably worthwhile having a knowledgeable Bahasa Indonesian speaker handling check-in who can forcibly point out to check-in staff that these bags have to accompany passengers on the same flight. If the flight is full (which is usually the case) and there seem to be a lot of bags being checked, it might be worth asking this person to prepay some sort of gratuity to the ground staff to order to reinforce this message and assure your peace of mind.