I was in the same boat, and have spent some time trying to familiarize myself with it. Here's what I know, and hopefully is in a somewhat simplified fashion/explanation:
The part you want to focus the most on, is located here:
That will have a folder full of configs populated with all the mods you have installed (at least, from ones that add some kind of entity to the game). There are exceptions to this rule, but that's going into another part of the config entirely (do some reading on the EntityHandlers for more info about that). For the most part, the EntityHandlers are automatically detected and configured properly. If not, or if you want to make a change to what spawns "naturally" using JAS, you'll need to modify those configs.
Since I'm not sure what part you're having trouble with, I'll try explaining a few things, but will save the great detail for the wiki to help you with. I've learned everything by trial/error, and by reading through the wiki, quite a few times I might add, until it finally stuck. Here's a small example from one of my configs from Mo' Creatures (MoCreatures.cfg):
That's broken down into 4 pieces:
Weight - The chance you want this mob to spawn
(I'm not a pro at this either by any means, but the way I understand weight is, add up the total weight of all creatures)
Total Weight: 33
Then, divide the creatures weight by the total weight, to get a percentage of how often they'll spawn. So in this case, foxes should have an 18% chance to spawn, vs. elephants which have a 45% chance. So, you should see more elephants than foxes.
PassivePackMax - The maximum number of mobs that will spawn together, when they do spawn
ChunkPackMin - The minimum number of packs of this mob that you want to spawn per chunk
ChunkPackMax - The maximum number of packs of this mob that are allowed to spawn per chunk
So, in the case of the above example, I want Foxes to spawn in packs of 2, a minimum of 1 pack per chunk, up to 4. Hopefully that makes more sense now.
You'll need to edit each of these configs for each mod you have that adds creatures, if you want to get it perfect. You can alternatively check how to spawn by climate type instead of by each individual biome, so that you're not configuring say, a Lion, for each individual biome, but instead for all biomes that would qualify as a Jungle, for example. I chose the longer route myself because I didn't find this option until I was already over halfway done doing it the long way, but I understand that when you configure by "climate" (there's another name for it, I think, but they mean the same thing) that it's much easier, and much faster.
The only other file I've really played with to get things right is CreatureType.cfg, which is at:
For me, the only things I changed were Spawn Rate, Spawn Cap, and in the case of the 0"Creatures" Group, Chunk Spawn Chance.
Spawn Rate - How often the spawn cycle is processed for the given group, which is displayed in Minecraft Ticks
Spawn Cap - Controls the maximum number of mobs allowed to spawn from any given "GROUP"
Chunk Spawn Chance - Only done the first time a chunk is generated. When you FIRST enter a new area and cause chunks to be generated for the FIRST time, entities are "chunk spawned" with whatever chance you've entered.
Let me know if this helps or if there's something I can try to explain better. Also, anyone feel free to correct me if any of this is wrong, but to the best of my knowledge, this is correct.
Thanks for taking the time to post that, and yeah it helps a lot. I am a bit burned out from trying to figure it all out myself but i will work on it again tomorrow using your advice. Will post my results.