they are marked on the map which one is which take a look plus they are different colors on the map to(the dots that represent each comp).
http://paragonwiki.com/wiki/Missile_Launch_Mission
Edit copied right from their "The launch computers are located in the sublevel of The WEB and are marked on the map as Biological Payload, Chemical Payload, and Nuclear Payload. The launch computer you use determines which temporary power you receive for firing the missile into orbit. "
So, the other day I was goin through Warburg restocking my blaster's nuke supply. I had the buff one already, so all I needed were the other two, but I didn't know which computer gave which code. I ended up having to use all three computers because I clicked the one I already had.
This made me wonder why there wasn't some kind of prompt window or warning or way to tell the three apart. I think it would be a nice thing to impliment into that system so that other people don't do this.