Questions about the Arduino Micro PCB
The 5V regulator is only used when you are powering from external power (>5V). The 3.3V regulator is only used by things that you power from the 3.3V pin on the Micro.

So if you aren't using external power you don't need the 5V regulator. If you aren't using any 3.3V devices then you don't need the 3.3V regulator.

You can use any micro USB or even mini USB connector you like. If you ignore the "ID" pin you can even use an old-fashioned chunky USB B connector like on the Uno. 

The circles are fiducial markers and are special patterns on the board used for aligning a pick-and-place machine when manufacturing.