If I understand your question correctly, there are two basis places to put these new .webm files to be used from Assets.
1. You put the V8 (converted) .webm file into your Campaign Images folder: ... SmiteWorks\Fantasy Grounds\images\[your campaign]
2. You create a Token .mod and drop that into: ... SmiteWorks\Fantasy Grounds\modules
It's fairly easy to create a Token .mod file, and there are a number of threads that explain this. Zaccaeus has some great Youtube videos, if I recall, that explain this and most of what you need to know.
From the images folder in Assets, you can use the .webm files as brushes through the Paint or Layer functions of the map.
From the Token's folder in Assets, you can use the .webm files for Spell Tokens or Tokens for NPCs or PC (obviously).
I have not yet used the .webm files to make full Map images. That's next. Good luck.

