[Fyron]

You do not need to set up AI empires on the PBW site, UNLESS they come before human empires. As long as all human empires are in lower player numbers than all AI empires, then all you do is assign each player to the proper empire name on the PBW site, and upload the turn files zipped up (don't forget .cmb and .log (or whatever the other 2 extensions are)) as AT said. If there are any AI empires between or before any human empires, you will need to set those AI empires up as human empires, using dummy player names, and then mark them dead.