USING THE BIOME-SPECIFIC TEMPLATE SYSTEM
Each biome has a folder from which the ruins mod will load its templates.  You can specify a particular template for a biome by placing it in the biome's folder.  The mod will also load ruins from the root rolder (<minecraft root>/resources/ruins) to be used as generic templates, which can spawn in any biome.

When the mod attempts to generate a ruin it first checks to see whether one is wanted for the chunk.  If so, it then checks to see whether it should use a generic template or a biome-specific template.  If it uses a generic template, only templates found outside of the biome-specific folders will be considered for random generation.  If it chooses a biome specific template, only those templates found inside the given biome's folder will be considered.

You can use this to your advantage.  If there are no generic templates only biome-specific templates will be available, so ruins in biomes will be rarer.  For instance, with no generic ruins, if you set the forest biome to use biome-specific templates 75% of the time then there is a 25% chance of a ruin not being generated even though it was called for in generation.  Similarly, if you use only generic templates you can tweak the instance of templates generating per biome by specifying the chance that a (non-existant) biome template will spawn.

THE OPTIONAL FOLDER
I have included several templates that do not fit the general "theme" of the mod, at least as I envisage it.  You can enable them by moving them out of the OPTIONAL folder into a biome-specific folder or into the root folder for use as generic templates.

Most of these templates include mob-spawners and treasure chests; I realize that some people might want to add the ruins into minecraft but not more dungeons.  The choice is up to you.  There is also the excellent GuardHouse template which I removed from rotation because it has torches.  If you are using a mod like Humans+, this is actually a good template to put back into rotation as it helps add to the atmosphere.