[Calahan]

My guess would be that all you'd need to do is change the CD-Key between submitting turns for your two nations.

1. Play and submit/upload your turn for nation1 using the CD-Key that came with your first copy of Dom3.
2. Exit Dom3.
3. Locate and delete the "key.file" in the Dom3 directory.
4. Start Dom3 and enter the CD-Key that came with your second copy of Dom3.
5. Play and submit/upload your turn for nation2.

My understanding is (although may well be wrong) that it is only the issue of identical CD-Key's that prevents the same person (or more accurately, the same copy of Dom3) from submitting turns for more than one nation.