how to manage fbx files animation (blender) in unity using favascript

It very unclear what you mean. Please write more details.

I don't know how to make the animation work. Every time the script run it glitch. And has to be in javasrcipt since the whole project is writing in it.

Which part doesn't work? Which function call? Can you paste some code. At the moment the answer would be: just read/watch some tutorials about how to build animated character.

This is a fast reply:

I will paste the code and thank you for your patience and suggestion.