On Thursday, September 10, 2015 at 7:53:55 AM UTC-7, Not@home wrote:
I had an extra seedling this year that looked pretty healthy, so I put
some stones in a pot (it is a big pot and I didn't have enough spare
dirt to fill it, so I put eight or ten inches of dirt on top of the
stones and transplanted the seedling to the dirt.

The problem is that the water runs through the dirt and stones and out
the hole in the bottom of the pot, so every day the plant, while it has
been growing well, loses the structure of the leaves (it almost looks
dead) until I water it, when it regains its vitality and looks healthy
until the next day. And the early maturing tomatoes have rather
advanced end stage rot.

So I am looking for a way to solve the watering problem for next year.
I am thinking of removing the stones and filling the whole pot with good
dirt, and burying a bowl at the bottom of the pot, reasoning that when I
water, some water will filter into the bowl and keep the plant happy.
I've been told that standing water in the bottom of the pot is not a
good idea, but I grow my seedlings in dirt over a tray of water, and
they grow extensive roots in the water.
[...]

Honestly don't see the problem. Put a big saucer under the pot so the runoff from your watering method will be saved.

Your idea of removing the stones and replacing with "good dirt" is a winner. Follow up with a big capacity saucer underneath and you should be home free.

Occam's Razor...

HB