EDIT after testing for myself in the default mod launcher:
I used two mods that change faction emblems and the one above actually overwrote the one below. It's pretty deceiving, considering in games like Skyrim its the exact opposite. But for Warhammer it appears the ones above overwrite the ones below. So the mod author is right that's my bad for bringing Skyrim modding knowledge into this.

If the mod author wants me to delete this I will, otherwise I'll keep it up for anyone else who was confused.

Original text (incorrect info):
If the mod author's intentions are to not let this mod get overwritten by anything, it should actually load dead last. Right when you open the game and go into the mod manager and hover over the number of a mod under the "Load Order" column, it will say something like "drag mods to change when they will be loaded when you launch the game." That's why its called a load order, mods at number 1 will be loaded first, and mods at number 100 will be loaded after every mod before 100.

So if anyone is having problems with this mod and has other AI mods, its because those other AI mods are being loaded AFTER (below) DeepWar AI. So if the other mods change the same files that DeepWar changes, it will overwrite DeepWars changes in favor of the other mods' changes.