With this mod there are a lot of different ways to play since there are so many changeable options. Because of that I wanted to make a guide for some of the most common ways to play the mod, for different playstyles and modpacks.
Note: these presets are not available in-game (although that is something I want to look into), this is simply a guide on common sets of settings.
"Disabled" means the enemies in the faction have enemy on enemy combat disabled, "Enabled" means combat is enabled as well as the faction alliances, "Rogue" means enemy combat is enabled but the alliances within the faction are not.

Just the default settings.
This entails that the enemies are split into a bunch of different factions, and that Mod NPCs will hurt each other, but the mod will try to detect for owners to make it somewhat more functional. Modded worms may not function here.

This is the true "neutral" experience, changing up the gameplay quite a bit, but is not too chaotic to overpower the mod. May cause problems with very large modpacks with lots of enemies, but works fine with smaller and medium-sized ones. Modded Bosses will work as they do regularly, and do not do combat.

EDIT: Modded Bosses are now set to Disabled by default! This means they act like they do in the regular game, and do not do any NPC on NPC combat!
Modded NPCs: Disabled
Modded Bosses: Disabled
Exactly the same, except Modded NPCs and/or Modded Bosses are both set to disabled. This makes the mod a LOT more usable with large modpacks and modded invasions. Is by far the most common change done and makes Calamity easier to use.

If you have problems with Worm Bosses, such as the Desert Scourge, just setting Mod Bosses (in some occasions Mod NPCs as well) to "Disabled" will fix all the problems.
This also helps reduce performance issues a lot if there are many modded enemies infighting.

The only real downside here is that modded NPCs and modded bosses will not be able to interact/combat base-game NPCs and bosses, but for some that may be a good thing.

The "Extra Factions" section has most by-default Rogue, making it so the factions do not exist in-game unless this is changed.
Some may feel there are in fact not enough factions, and that too many of the game's enemies are hitting each other. This also helps with minor performance increases so that may add another motivation.
This makes the game less chaotic, so those who like that may also want to Disable Mod NPCs and Mod Bosses as well.

This is just my initial draft, and I will update this guide to clean it up/add more common presets as needed/requested.