Yeah, the best solution would be a dedicated server for the online play. That would mean you would use the third machine for the server or -if that PC has a dual core- you could combine the IL2 server and Il2 game on one machine since I don't think the dedicated server will need much processing time with only two players.
How?
See here for the dedicated server:
http://pacific-fighters.com/en/updates.php
I think instructions are included, if not, look here:
http://forums.ubi.com/eve/forums/a/t.../692106434/p/1
You will need to install it seperately and apply the latest patch. With a script you can have the server run all day, automatically restarting the game. You could also rotate a few missions all the time for variety. The two networked PC's will only need to connect once -at the start of the day- and then do not need attendance, provided that no-one exits the game (prevent using the esc key?
).