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Potting plants in the aquarium

I recently moved my plants from a 20 gal into a 55 gallon tank. I had a few 
amazon swords which I decided to pot to make arranging easier and less 
stressful on the plants. I am using clay pots which I pre-soaked for some 
time, with peat on the bottom, some potting soil with plant tabs, and gravel 
on the top. The 2 plants which I potted seem to be deteriorating, though some 
offshoots which I planted in the gravel (quite small) seem to be doing fine. 
I don't know if they're acclimating to different conditions, or if potting in 
clay is not desirable. I'm wondering whether the lack of circulation through 
the substrate, as it would receive if planted only in gravel, would be 
detrimental to the plant, or cause rot. Any advice on potting would be