I think with either kind of pickup it helps to let go of any preconceptions about what your guitar ought to sound like, and work with what it actually does sound like. And we're talking damage control here -- you want the least-bad version of your current reality.
Also, I think it helps to be mindful of your audience and what they came for. They're there for music, and they'll probably like your music better if your instrument's sound fits in well with your voice and/or bandmates. The butts in the seats really don't care whether or not your guitar sounds like an accurately-amplified version of its acoustic self. Except for that one guy with his arms folded who can't stop staring at your fingers. And he's probably reading this. :-)
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