I think three boxes can narrow down to two points if one knew: The exact time it originated, and the speed of the effect, otherwise more boxes would be needed. (Normally three satellites and a precise clock can be used with GPS, otherwise four satellites are needed. However, with GPS you know the speed of light.)
I'm not precisely sure of the following, but I'm assuming someone will correct me if I'm wrong:
(Assuming that the boxes are placed in a proper configuration, e.g. not in a line/plane, etc)
Two boxes: Tells you which box was closer to source.
Three: Locate on a plane
Four: Locate on a line
Five: Narrow down to two points, and determine speed of effect.
Six: Locate precisely with speed of effect.
It's also possible that if the clocks aren't accurate or precise enough more boxes could reduce the error in locating the source. If there was more than one source even more boxes could be needed to find all the sources.