My my my... where to start...
A complete servo system consists of four components : controller, driver, motor and encoder.
The driver is an amplifier. At it's simplest, it takes an analog voltage (some can be configured for step - direction, or pulse train as you call it) and will go hither and yon as instructed. Analog will move with a speed or torque based on the voltage amplitude applied, and direct based on polarity, ie +10V = max speed forward, -10V = max speed reverse. This versatility makes it a bit more popular.
The encoder does a whole host of things. It tells the driver where the motor is in it's rotation, which lets it determine which coils to energize to move the motor or hold position. It also provides pulse feedback, which can be passed on to the controller.
The motors really aren't that special in themselves, as long as they are big enough to move the load. They are constructed to work with the drivers, and have the encoder built in. The position of the encoder marker relative to the angle of the rotor is critical - if the encoder goes bad, the whole unit must be replaced in most cases.
The last element is the controller, which is what you seem most interested in. The controller takes the pulse train from the encoder, plus a home switch and the encoder marker, and can determine absolute positioning ("go to 10000 counts" as opposed to "go 1000 counts clockwise"). Some have presets that allow you to automatically home the motor, or program movements of certain distances, or movements at preset speeds.
To muddy the issue further, some drivers have the controllers built in - the electrocraft IQ2000, for instance - and are fully programmable. The IQ has inputs and outputs on board, making the PLC completely unnescessary. Others, like G+L DSM series, have limited I/O for presets, and must be controlled by a PLC. DSMs have a port to feed the encoder position back to the PLC, making the PLC itself the controller. This feedback is usually so fast, a special servo card is required - think about it, your controller controls the controller that controls the control that controls the motor
This was an awfully broad overview. I suggest looking at the DSM line and the electrocraft IQ, they represent both ends of the spectrum. It's a difficult subject, but very rewarding and useful.
Happy Hunting
TM