Desired number of good/evil square count in S/M/L sub-regions?
That. If you want massive evil areas, raise the third number, Large regions. If you want craploads of evil pockets in the midst of other biomes, jack the Small region number up.
Are you sure about that? My understanding was that the numbers here determine how large (in tiles) in respective region is, meaning that in a game with 9999 under the small area parameter, a small area will be 9,999 tiles...
It's mostly dependent on how DF defines Large, Medium, and Small subregions. Running a few quick tests on a pocket region, setting large evil to maximum (and all others to none) didn't get any results, but setting small to max did. Which probably means that the standard pocket region doesn't have any large (sub)regions. (Note that the only things I've changed are the Evil/Good settings, nothing else.)
Moving up to the standard Medium Region, again with all settings to none except for Large Evil to max. The evil areas are incredibly huge, but there are no evil pockets to speak of. Switching it around, with Small Evil to max and the rest to none, there are myriads of evil pockets spread throughout the map.
Same thing happens with Large Regions, too.
That technique is how I gen worlds where glumprongs and feather trees within the same 3x3 or 4x4 embark area.