This is a multi-step process. First, you will need to decide if you will either a) add your new stone layer to inorganic_stone_layer.txt, or b) create a new file in the raws folder named something like inorganic_stone_layer_StagnantSout.txt (or any file name you like). If you do the latter, the first line of the text file must be the name of the file without the ".txt", and the next needs to be [OBJECT:INORGANIC]. The second option is generally considered cleaner.
Then you'll need to define your layer stone. Give it a name, like "Sillystone", and change the raws of an existing stone to describe its color, tile, physical properties, etc. Note, you must define the stone layer as one of [METAMORPHIC], [SEDIMENTARY], [IGNEOUS_INTRUSIVE], or [IGNEOUS_EXTRUSIVE]. This is necessary for the game to understand the inorganic being described is a stone layer, but will cause problems for your next step.
Finally, you need to go into the raws of all the minerals, gems, etc, that you want to appear in your layer and add an [ENVIRONMENT_SPEC] tag to each of them to appear in Sillystone, for example: Native Gold would be modded to include [ENVIRONMENT_SPEC:SILLYSTONE:VEIN:100], which will make veins of native gold appear in sillystone. Your choices to replace "VEIN" are VEIN, CLUSTER, CLUSTER_SMALL, and CLUSTER_ONE.
Now, there is where your problems lie. Some minerals and gems are set to appear in all stones of a layer, not specific stones. For example, cinnabar (which is not particularly useful in game) appears as veins in all igneous extrusive layers. You could conceivably go through every mineral and gem and change their raws so that they will not appear in the layer type unless they're a mineral/gem you'd want, but that'll be a lot of effort; although, as you're already going to need to go through all the raws anyway, it might not be as much extramwork as I'm thinking.