When you start up a new world (Havent tested in Multiplayer yet), upon entering the nether or Aether (and I assume End and Twilight Forest but not tested) they use vanilla particles until relaunch in that world. So if you relaunch the world in the Aether, FBP will load there and in Overworld, and if you later enter and relog in the nether particles will be shown in all 3 dimensions. Not the most important thing in the world I know but I thought it should be mentioned.

For reference: TominoCZ/FancyBlockParticles#123