I used it for the first time this week and while I did get some debris out I really feel like it would be more effective to stir up the gravel and let the water drain. I was cleaning a 5 gallon. I have to be honest and say with trying to work around the decorations and not move them that it was tedious and I just didn't feel like I was doing too much good. I am not taking my fish out during the process I drain the water so the fish has just enough water to cover with. He is devil to catch and I don't want to injure him.
Yes, stir and dip or even stir/siphon will work-You don't want or need to try and get all the mulm/debris out of the tank-some is need for the microorganism that help keep the tank healthy-Since its a closed system we need to make the water change-but you don't want too clean and sterile since that is hard to support life.
I pump the siphon up and down in the gravel, it loosens up any debris and sucks them up. But, you are right, there is still some stuff left in there, but my readings keep coming up correctly, so I'm assuming that as OFL said, it's good. :)