Common ground and voltages
One key concept that might help in clarifying any misunderstandings is this:


A voltage is the potential difference between two points in a circuit, it is not an absolute value of any physical characteristic at a single point in a circuit. Thus, there is no absolute potential involved, it is relative value, a difference.


How this applies:

The "ground" of the Arduino is the point (or PCB trace, to simplify the concept) relative to which, the potential on the "Vcc" trace of the Arduino is measured. Thus, when powered by the USB cable, the Arduino's "ground" is the measurement basis, and is incidentally at the same potential as the "ground" of the computer whose USB port is being used.

The "negative" of the battery is merely one of two points across the battery, between which the potential difference i.e. the voltage of the battery is measured. Relative to the rest of the (electrical) universe, the "negative" terminal of the battery is floating, i.e. has no specific relative value until this so-called negative terminal of the battery is connected to a circuit. 

When you connect the negative terminal of your battery to the ground of the Arduino, you are providing a reference value for the battery, relative to the Arduino. Thus, only while such a connection is made, the "positive" terminal of the battery is at a potential of "battery voltage" compared to the Arduino's zero level or ground. 

If, instead, you connected the battery "positive" to the Arduino ground line, then the other terminal of the battery would be at a negative value compared to the Arduino's zero level or ground.

The battery, or for that matter any arbitrary voltage, is relative to the reference you provide. It is a difference, from your defined base point in the circuit, not an absolute value, to reiterate the basic principle mentioned at the start here.