Have you edited the army with Wh32Edit? Because the program doesn't support army header editing and so the Banners will be wrong in the troop menu if you havn't used a greenskin-header.
I hope you will extend the campaigns. As a new feature i thought about the map: Ghabry have anywhere a tool (or a tutorial) how to change the points on the map (where the army moves from town to town). Perhaps you can ask him.
I don't have a waypoint editor (only a cheat to view them ^^). You can only change the auto deploy position.
Or do you mean the overworld map? Look in the GameData\GameFlow Files with a hex editor. The values in it are x-y-coordinates (for line drawing). You can modify them to change the path they walk between the mission. (Maps are in Graphics\Maps). No tool for easy editing available, sorry :/. You can view them with the DOT-Viewer I created some moths (years?) ago. It's not the best viewer but better then nothing (the lines should be correct, except World 4 which looks strange)