HOW SIGNALS WORK

As the train passes from block to block, the signal at the beginning of the block turns red, but the trip arm remains down.
When the last car of the train leaves the block, the stop arm goes up.
When the last car of the train leaves the second block, the signal turns yellow and the stop arm goes down.
This insures that there are at least 2 red signals and one raised stop arm behind the train.
When the train leaves the next block, the first signal turns green.

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New York City Subway Signals
New York City Subway Signs
New York City Subway Chaining Codes
Train Whistle Signals