I think I see the problem. A false bottom is meant to circulate--what you need is only a drainage area for the substrate if you are not using this layer of water for the purpose of a water feature. Drain it entirely and leave it that way. You have no reason for having a dead layer of water under your tank substrate otherwise. It will then be just a drainage area for the substrate on top and you can siphon off any excess water that seeps down into it. When I either have a self-contained fountain or some other water feature on top, I don't build a false bottom at all, but only a drainage layer of gravel and perhaps some charcoal beneath the substrate, and siphon this off only when it accummulates enough water from misting, etc. to seem to need it, which is rarely. You do not need a layer of water under your substrate for any reason unless you are utilizing it as part of a waterfall-stream-pond-circulating system. All it is doing now is creating a stagnant anaerobic condition that smells like sulphur. Drain it.

As far as the plants are concerned, they will do fine--just remove any that don't. You won't have the same sort of poop/excess food recycling system with a snake as you would with dart frogs, but neither do most plants that do well in terrariums need high levels of fertilizer. You may be surprised how well they do without it. You can merely top-dress the substrate with another layer of leaf mold, organic compost or whatever occsionally--maybe once a year. This is not the same thing as growing vegetables, or even keeping house plants. As far as the gnats and flies you are worried about, just ignore them. They will be a part of the system and either cycle out or help out. They aren't pathogenic, except the sight of them might disturb your sense of sanitation.

Keep the right conditions for your snake temperature-wise, humidity, ventilation, and then remove any plants that don't take to the same conditions your snake requires.

I think you have somewhere been misguided by our passion for false bottoms, and the fact that perhaps I'm not the only one who has misread your posts. My advice is not to sweat the various flies, fungus gnats and such that are rather natural invaders of your tank--do not introduce any sort of insecticide, whether touted as "organic" or not, and just continue setting it up. The bugs will cycle out in time. Don't worry about plant nourishment diminishing. Just set it up with your snake's welfare in mind. It will work. But do drain all the water from the "false bottom" and use it as a soil drainage area instead. There is no reason you need water down there if it isn't part of a circulating system.

Anyone else still here? Am I giving bum advice? Josh--where are you?
-----
Patty
Pahsimeroi, Idaho

4 D. auratus blue
5 D. galactonotus pumpkin orange splash back
5 D. imitator
6 D. leucomelas
4 D. pumilio Bastimentos
4 D. fantasticus
4 P. terribilis
4 D. reticulatus
4 D. castaneoticus
2 D. azureus
4 P vittatus

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