iPhoto and separate folder - Overkill?

I am currently using iPhoto 11 for my 9,000+ pictures and movies. Currently I have my entire iPhoto library stored on a portable hard drive (to save room on my MacBook Pro) and I also have a folder that contains all the .jpeg images separate from iphoto library, in case I want to show the photos on my son's windows computer. I am considering moving to Aperture. Would I still need to have a separate folder with just my .jpeg images? It is difficult to remember if I have loaded to pics into both places and it may be just overkill. Any thoughts?

Thanks, Roxanne