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Just know where you place the root tabs and try to go around them I guess. Or just don't go as deep with the vacuum when doing those areas. I always hate when mine come up!
I don't vacuum the bottom of my planted tanks. The mulm and detritus (organic material) that collects on the bottom is very good for the plants. It dissolves in the tank water and provides nutrients. This really saves money on fertilizers and by not vacuuming, I don't disturb the substrate or the plants.