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Depends on the plant. Usually I have a layer of gravel then a nice couple inch layer of dirt to go with it in a planted tank (dirt well above water line). In this set up it doesn't matter if you keep them in a pot or not, but why would you really want them to stay potted? I'd rather have them root and spread unless there is some reason you will want to remove them easily.

Most of the time now I just go with a layer of gravel, a layer of sphagnum moss, then cuttings of vining plants that root in water (philos, syngonyms, ivy, pothos, peace lilies, the semi-aquatic wet roots kind of plants). Not all plants handle this well. Even if you still have them in pots, if the bottom of the pot is below the water line the plant will rot unless its like the above mentioned type.
 
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