You just do the shallow or no disturbance close to plants, whereas in open areas you deeply clean the gravel. Sometimes people pull their decorations and clean underneath but most people do not do that all the time. Plant's toleration of being moved varies by species.
I have the eheim gravel vac and it works very well. I vacuum daily as Im currently supplementing my goldies diet with duck weed and it goes through them like a vindaloo following a drinking session!
I try and distrub the gravel as little as possible and alot of the time just remove the surface debris. I've found that if I dig to deep it chucks up a lot of suspended solids into the water which I actually think is from the substrate. Its like when you wash the gravel for the first time (but no way near as bad). I did a little bit too much last night and one of the fish appeared to be 'gasping' in the water a little due to the suspended solids until they settled down again.