For ALL of the small seams that I have to fill, I use Testors glue (in the stand-up container). I assemble the parts normally, then sand (lightly ) Afterward, I will wipe the area off with a slightly damp cloth. This removes the dust particles, embedded in the seam and gives you a better look at your work. Just blowing off the part doesn't get it all out of the seam.
If there is still a seam visable, I will run a very thin line of the glue on the seam. I will let dry overnight, then sand.
For larger seams or gaps), I use Squadron's White putty.
It sounds like a lot of work but, as you said, it makes for a much better looking piece.
There's nothing worse than, getting that first coat of paint sprayed on your build and discovering a seam line in plain sight