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Do you mean Gravel vacs? If so I generally don't vac where my plants are, I let whatever drops there decompose and let the plants use it as nutrients.
You could hover the vac over the plants to remove some waste.
Personally I hover over the gravel wherever I can easily get to and suck up whatever is on the surface. I don't disturb the gravel or the plants themselves to try and get any more and it never caused any problems. That is until you pull up the plant and then all the 'stuff' comes up with it. I found having a vac at the base of the plants gets most of it before it clouds up the water too bad.
I do it just like super... wave the vac around and in the plants to suck up whatever I can. I don't worry about the gravel too much as in a heavily planted tank, the plants are pulling PO4 and NO3 out of the substrate as fertilizer.