Sadly, the exporter doesn't support exporting multiple animations yet. (And I have a feeling that it never will. For some reason nobody is willing to work on the code anymore. I would if I was a coder.)
You have to export a separate json file for each of the animations your character has, and then combine them manually in a text editor like notepad++. It's pretty self-explanatory if you just take a look at the model files from some of the Q3D example files, like the Quake-style mercenary guy.