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The way I always saw it was the the coordinates were for the 3 dimensional galaxy. One for "height", "width", and "depth". Each point would make it possible for Starfleet to pinpoint Voyager's location fairly precisely.
------------------ "We choose to do this and more. Not because it is easy, but because it is hard." -- John F. Kennedy
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Frank is correct. As the TNG tech. manual states, instructions can be input in coordinate form, but it's quite a hassle. Still, it can be very useful depending on what you're doing.
------------------ "And though I once prefered a human being's company, they pale before the monolith that towers over me." -- They Might Be Giants