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They triangulated it using the three microphones I guess. Also I guess you can figure that out by looking at the debris pattern because they seem to have a lot of knowledge about the used rocket.

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There were actually four microphones - captain, first officer, cockpit and observer (see page 46, Figure 9). Four receivers is sufficient to determine the sound origin at a point in space, with an associated error volume (three receivers only allows you to determine a curve in space).

See https://en.wikipedia.org/wiki/Multilateration

The problem is complicated if we consider that the missile is moving at supersonic speeds (~mach 3 + aircraft speed).

I don't know much about supersonic fluids. For anyone interested in following this up, here is a paper on "Reproduction of Virtual Sound Sources Moving at Supersonic Speeds in Wave Field Synthesis":

http://www.researchgate.net/publication/230702229

They did that and they also used string to track back from the impact sites to a rough point in space.

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