Do you mean particle emitters or a single emitter that's spread all over?
Depending on what you want to do there's a couple different ways.
a) use a script to randomly spawn particles in the area you want & use the "saveparticles" command from the console to save those to the .map file. Just don't run the script again.
b) use various layers in a single emitter (or a several emitters) to achieve the look you want.
c) don't use particles, use a model. You can export your map to a .obj & use a 3D program (like Blender) to "paint" your particles where you want them, convert them to polygons, then export all those as a single model.
I've done b& c before.