Oh word? Well that's dope you figured out how to get it to work!
I'm pretty sure your shotgun records stereo, most do at least. But I could be wrong. Best way to check is just watch your audio levels and look for both channels to be working. Try dropping one channel completely down, and check to see if the other is working, then do the same to the other channel. These kinds of things happen all the time though, as I'm sure you've already figured out hahahaha. That's what we get for working with electronics... Also even with mono tracks, FCP will bring in two audio tracks no matter what, kind of weird, and an annoyance, especially in a situation like what you had.
Also, if you haven't already, you should invest in some good headphones. They make such a difference when shooting, and you can catch audio problems immediately (peaking, interference, low levels, etc...) You'll hear John Marsh say "Great audio can make terrible footage look amazing" at some point in school.
But keep it up man, you're picking things up really quickly