We have some real plant experts here on the forum, and I am NOT one of those, but....here goes.
From what I understand, you don't vacuum the substrate of heavily planted tanks quite like a regular tank. Just as you say, you move the vacuum over the top, and pick up what you can.
You also don't go to the limits on fish population, this helps to keep the excess waste down.
MTS snails

are used to move through the substrate and this eliminates gas pockets, or you have to use some tool every few days to slightly disturb the substrate to keep pockets from forming, being very careful to move it under rocks or other decorations. The low fish population / careful feeding keep MTS snails from taking over, or you add a few yoyo loaches!
