But, corret me if I'm wrong I haven't played in AGES, you can only put instant cards on the stack after it is already started.

You could store each individual set to a differet program and to make the different sets compatible you could make it so that each players deck is copied on the other calc before being played.  I recomend by starting by making a simple version that only allows cretures with no abilities and one type of land and adding more as you work on it.