What not to use in the substrate

First, what not to use.

Carbonates are out, generally speaking. The substrate in an aquarium generally should not contain calcium and magnesium carbonates. The exceptions are biotopes that you set up specifically to provide a strong calcium and magnesium carbonate buffer in order to stabilize a high pH. These characteristics are suited to unplanted aquaria planned for African Rift Lake and Lake Victoria cichlids, and to set-ups for some livebearers or Central American cichlids, which also prefer hard alkaline waters. Brackish aquaria would also require high pH in addition to their salinity. In all these setups, a percentage of marine reefkeeper's aragonite, composed of shell and coral debris, makes a useful addition to the substrate. It may be called "crushed coral" and you might be able to buy it most inexpensively by the pound, scooped out of an open bag at your LFS. Alternately, several kinds of pre-packaged aragonitic mixes designed for marine aquaria are available. Don't hunt down the specially-prepared aragonite that's been ground to a powder measurable in microns, for an almost-instantaneous pH boost. It's too fine and too fast-acting for your purposes. And it's too expensive too.
 
Sea sand is out, because, even after all the salt has been rinsed out, it contains shell fragments that will raise the pH. Its silica grains are rounded from much wear: sand from the beach could pack down more densely than you want  ...or are those my old "compacting fears" acting up again? 
 
Sand from a sandbar in an unpolluted stream would be fine. Don't boil it to eliminate generic "nasties:" a couple of insects might hatch; your fish will eat various minute critters; any surviving bacteria will merely add to wholesome biodiversity in your system. Don't choose the sandbar just downstream from the old chromium-plating factory, eh.
 
Nowadays I avoid gravels with epoxy coatings, even the natural looking ones. But I have some of these fine-textured brown "aggregates" packaged for aquarium use, and they still look fine after almost ten years. If any of the epoxy coating has ground off over the years, it is chemically inert, after all, and it has wound up in the filter medium anyway.
 
It's too easy to be cruel about pearlized gravel and other Futurama effects, so I won't even mention them.
 
In the lower layer you should avoid organic matter that will rot under anoxic conditions. It is important to understand the difference between compost and humus in that context.