Markacres-
The manual properly describes how PBEM should work. One player generally is the host and the other player(s) participate. The host will send the players the appropriate trn and rpl files (no rpl file at start). He will receive back the ord files. At that point, assuming the host has generated his orders for the turn, he can execute the turn and the process begins again.
Alternately, there is a bilateral hosting process where players alternate as hosts that also works quite well for two player games. The process is described in:
http://www.ageod-forum.com/showthread.php?24142-A-method-to-speed-up-your-PBEM-gamesGood luck!