Kymmie's point is well taken, and there are others to consider. Unless you have a specific reason for having your aquarium plants in individual pots rather than in the substrate, it is not advisable. It is useful with certain fish that tend to uproot plants by moving the substrate at their whim, and I have known Discus
breeders to use pots to keep a bare substrate. But other than for specific reasons, plants will be better in the substrate, although this depends upon the specific plant species.
Substrate-rooted plants that have extensive root systems such as Echinodorus are best in the substrate. A mature Echinodorus bleherae
can have a root system that extends more than a foot in all directions from the crown of the plant, and while I have never experimented with these plants to see what if any detriment occurs if they are forced into pots, I would expect the result to be similar to terrestrial plants like houseplants that get root-bound.
The other issue is the complex bacteria cycle in the substrate. Water is flowing through the substrate, carrying nutrients; aerobic and anaerobic bacteria break up organics into nutrients. Plant roots assimilate those nutrients, producing oxygen that feeds the aerobic bacteria. Even the anaerobic bacteria has a purpose and needs to be there (in the so-called "dead spots" which are actually anything but dead). Allowing the plants' roots to freely spread out through the substrate is going to mean a healthier substrate and that means a healthier aquarium.
Concerning your desire to re-arrange the furniture, so to speak...with most plants that is not a problem. Stem plants obviously care not a tad, nor would plants attached to rock or wood where the object can be moved. Substrate-rooted plants are generally fine with some movement, as long as it is not excessive. Some authors even suggest pulling swords up regularly and trimming the roots to invigorate them or control their size. As long as the sword plant has a few weeks between shifts it should be OK. Crypts are a very different matter; moving a crypt can cause a meltdown, and while the plant usually recovers within days or weeks, it may not.