Most emitters that work in pI3 will work in pIAE. (pIAE and pI3 load the same emitter library files, including the Pro Emitter Libraries).
Although pIAE will give you access to a large number of parameters so you can do quite a lot of customization of the emitters in your After Effects project, it won't give you access to every setting. (pIAE won't let you change things that are in the various pages of the emitter properties dialog in pI3.) Therefore, you will need to use pI3 when you want to make changes that you can't in pIAE (color gradients, particle images, image reference points, initial angle settings, adding particle types, and so on).
You'll need to use pI3 to create new emitters, create new libraries, or move emitters between libraries.
There may be some cases where you may find that using pI3 is actually faster and more convenient than using pIAE (in complex compositions for instance).
There will probably be some maximum number of emitters you can add with pIAE, but pI3 doesn't have this restriction
I felt like trying to answer this for you.I belive this is what you want.I don't truly know much about Partical Illusion,I'm using the trial version.So don't wish for me to catch fire If I got this wrong. (HaHa!)