A lot of things in this hobby aren't concrete. aka There are many many ways to achieve what you're looking to do but there are always some guidelines that are pretty common and available if you've researched enough.
I would worry about making the entire bottom with gs/silicon because some plants prefer dirt. But, it's all how you want to do it. A simple ms paint diagram or something more of a spectacular sketch up will really help with your initial building questions.
It's always pretty cool to sketch out what you want and then look back after all that time and see just how close you got things.
Anyway, Good Luck.
I've made a water fall out of greatstuff and silicon but are you talking of the entire bottom or just a part? Are you going to pot your plants?
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