Using the indoor planter pots is actually a pretty decent way to discern whether the special and rare seeds you get are trees as they are not plantable in the pots. Otherwise, I've found the normal interaction of clicking plant on the seed or foods and choosing the plantar instead of the ground works quite the same. That being said, a few friends have been having trouble using the planters.
I put them in a greenhouse of sorts and put sprinklers in with them, however with floor tiles you get puddles - but using the restoration ritual that a witch gains at the higher levels takes care of that in a snap, as does bonehilda or a maid.