How to connect a 2 cell LiPo batter to Arduino Motor Shield?
From the Motor Shield page,


  External (non-USB) power can come either from an AC-to-DC adapter
  (wall-wart) or battery. The adapter can be connected by plugging a
  2.1mm center-positive plug into the Arduino's board power jack on which the motor shield is mounted or by connecting the wires that lead
  the power supply to the Vin and GND screw terminals, taking care to
  respect the polarities.


So they provide the screw terminals for a battery, you should be able to insert two wires from your battery/pack into the terminals. If your battery has a connector on it, you'll need to either cut it off or find an adapter.

Be extra careful: if you have exposed leads from your battery and they touch, it'll get extremely hot and possibly catch fire.