Just so we are clear: You are building a vivarium for thumbnails, right? And you have a circulation pump because you want to have a waterfall, right? Are you going to build a backdrop where the water will fall on it?

For your pump, and I do not know how your viv is set up already: make sure it's secure on the bottom glass. Ideally, you want to install it in a way that you will have easy access to it. For many possible reasons: water flow debit, replacing it, ect. If you want to prolong the pump’s life, there should be a filter between the pump and the water. If you buy a filter sponge at your pet store and place it between the pump and the water, it will do the trick. You could always use eggcrates to create a wall around your filter, and like MikeM670, use landscaping fabric on the eggcrate to filter the water before it reaches the pump. (I’m French – writing English is a challenge for me). Or refer to Cheri's suggestion just above.

For your drainage layer: Put minimum 1 inch (I like to put 2 inches) of hydro balls as your first layer. Then place your mesh on it, and it should cover all the bottom layer (make it about an inch larger on all sides, it will help keep the substrate in). Now if you are going to have plants, put your planting soil. Don’t be shy, 3-4 inches, if not more (again, I think you are working with a 12*12*18, so space is limited). Over it, you could simply add a layer of coconut husk, or jungle mix. Now get yourself some leafage, oak leafs, and put it on top of the coconut husk/jungle mix. And voilÃ*. You have to make sure that the roots of your plants have room to grow in the planting soil, and that they do not touch the mesh and mostly, the water. Your roots will rot and your plant will die. Now your enclosure must remain very humid for your thumbs, and you will see that even with a drainage layer and hydro balls, water accumulates. Keep an eye on it. (Because I live in Montreal and we have s*it weather, I have a heat cable on one side of the enclosure’s bottom glass, underneath. It’s actually fantastic for me as it evaporates the water.) If the water gets too high, and starts infiltrating your planting soil, siphon it out with a tube. Your plants should be very happy this way.