Let's take a given range of frequencies produced by, say, an acoustic guitar--the way that our ears naturally interpret those frequencies offers us some clues as to how we might make EQ adjustments on our amp or preamp box. The frequencies that our ears are most attuned to exist in the midrange. Thus, when we plug our acoustic guitar into an amp or PA system (with the system's EQ set to flat), typically a cut (or decrease) somewhere in the range of 200hz-1500khz will yield a more natural and balanced response.
Of course there are other factors to consider when tampering with your EQ--at what volume are you playing? Are you a singer songwriter, or are you playing in a group/ensemble? (More on this in my next post!)--however, I have found through personal experience that most acoustic guitars have what I might call a "naughty zone" in the middle frequency range (more often than not in the high-mids) that can be managed adequately with a bit of tone shaping. Try sitting down with your Fishman Loudbox amp or LR Baggs DI sometime and listening carefully to what those little EQ dials do. They were put there for a reason, so why not use them?