I'm not sure what you've got, but you do need a drainage layer of some sort, whether it's clay pellets, rocks and gravel or some other coarse medium, and it should be about 2-3 inches deep.
(Or a false bottom if you have waterways.) On top of the gravel layer, you will need something like weed cloth or recently, I've been using polyester batting such as that used in quilting. Just a layer of this will keep the dirt and such from filtering down into the gravel. Then when excess water accumulates, you can just siphon it off with a length of aquarium airline tubing. I use a shorter piece of larger tubing, perhaps 1/2 inch and run this to the bottom in one corner and let it rise above the substrate somewhat. It can be plugged with a piece of cork, or whatever fits. Then when you want to remove excess water, you can just run the airline tubing down into this and siphon it off into a container. The 60cc veterinarian syringes with cannula tips fit right into the airline tubing perfectly, so that you can begin the siphoning with one of these. (Then water your Rex begonia with this.)

I've never tried the clay pellets myself, mostly because I don't like the looks of them from the outside, but I imagine they are a lot lighter than gravel if you are concerned about this.

Again, putting in a layer of sphagnum moss--long brown, not peat will help prevent rot and enhance drainage. If this is for darts, you don't have to worry about them ingesting it, but I've read that it should be under the soil for other frogs that might gulp down a piece of it when feeding.
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Patty
Pahsimeroi, Idaho

Dendrobates: auratus blue, auratus Ancon Hill, tinctorius azureus, leucomelas. Phyllobates: vittatus, terribilis, lugubris. Epipedobates: anthonyi tricolor pasaje. Ranitomeya fantastica, imitator, reticulata. Adelphobates castaneoticus, galactonotus. Oophagia pumilio Bastimentos. (updated systematic nomenclature)

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