1...2...3...
What am I doing you say?.
4...5...6...
I'm counting down how long until someone tells you to put your game on PBW. .
Of course you might not want to use PBW, in which case sorry I can't help.
Once all your players have sent in their EMP files, you can download them all as a zip.
Then you start SE4, add the empires from the zip in order of player number and begin the game.
Upload the .gam file through the admin menu (AI/minister face) and then you're pretty much done. After that you should only have to do admin things if something goes wrong or if you need to tweak settings.