Glad to help!
Many times you don't need the two cores, there are enough good command cards that are faction/alignment specific that you can play a lot of good games without the overlap. However, there are some cards like Eager Troops that fit into many army builds. For situations like that, I really feel like using a proxy is the best way to go, just slip another card and a slip of paper with all of the stats from the needed card into a sleeve and play as normal.
This way, no one can say that they just didn't get the strategy they really needed to make their army work.
One thing I will say though, if you really like this game and get deeply into it, a second core set is really a great investment. Not only will you be able to get rid of the proxy cards (except possibly for 3 and 4 player matches), but you will be able to play mirror matches if both of you should want to play the same army. Also, it really opens up some interesting army builds, including the dreaded double Blood Thirster build. Not to mention a lot of other benefits. This is one of the few games that I really felt like buying the second core left me with almost no wasted parts.
I hope you guys enjoy the game. It has quickly become one of my favorites. If you find yourself with a lot of questions, BGG has some good threads, but I think you can't beat Sniper Toll's blog on the game. It covers a lot of basic game concepts in great detail.