Here's my step by step (I have extracted all of everything from all archives a long time ago):
1. Change the effect path in the animation file's CreateEntity code in Notepad++. If it doesn't HAVE an existing Create Entity, add a line break after the very last "?" character in the animation file and put the createentity code there.
2. Save to my mod's Documents/CustomMaps/Mod/source/whatever directory (not working directory).
3. In ArtManger menu bar click on Archive -> Build.
4. Navigate to and add animation in the CharAnimationTable or the monster's animation slot.
5. Build mod.
I don't bother moving anything when I build, so when ArtManager prompts to delete animation files on the first build after booting it up, I just click "No to all".
If there's anything I want deleted from the archive, I click "No" on every one of the hundred or so animation files one-by-one until it prompts for the file I want to delete

Not efficient, but I don't delete much at this point.