Keep in mind that guitar is a transposing instrument i.e. music as written for guitar isn't the same as music written for another C instrument. Middle C written on a sheet of music, middle C as played by piano, is an octave higher than the middle C we read. Middle C as played by a violin is the 2nd space from the top read by a guitar, but read by a violin its below the first line on treble clef. I don't remember which note u guys were asking about, but it should be clear now.
As for which one you play, well its up to you. As long as you are in the right octave, the fingering is up to you, which can make guitar a very hard instrument to sight read for, as there are usually many different fingerings for a given passage.