I always find plague pits and the black death morbidly fascinating! I came very close to working on one once too...
When I was studying archaeology in Uni, I worked on a Roman villa a few miles out from Brighton, which was basically in the middle of nowhere and was all fields and a few farms dotted around, and a church on the top of a hill.
The vicar at the church had asked a few of the students if they would do some digging in the graveyard before a Sunday school extension was added so the builders didn't come across any nasty surprises.
While digging up there we found several unmarked graves (most being of babies born out of wedlock!) and there was a part of the graveyard that was slightly raised. One of the head archaeologists on the site told us that it was probably a plague pit, and the reason he said that was because even though this church was in the middle of nowhere, it wouldn't have always been as villages and towns were built around churches. Something must have happened in the town for it to completely disappear and the theory was that it was wiped out by plague or moved a few miles away!
So apparently that's how you tell where the black death had hit: if you find a church outside of a village rather than in the middle of it, as the villagers moved off to try and escape the plague!