Hi,
You need to experiment as far as prefabs, I am not sure what's best.
As for the hick ups, start with a very simple particle system firing one particle at a time, and then debug properly how your collision is handled, by firing at a specific game object one at a time, if you try to do it all in one go it will be difficult to debug.
Particle collision are absolutly exact, so something is not quite right yet.
bye,
Jean