H bridge Circuit, Should I Tie grounds together

Im building a simple transistor h bridge circuit to control a dc motor, Now eventually when I put together the robot, ill use a 9 volt battery for the motor, and have a 5v regulator circuit for the arduino, and the grounds would be tied together. But while Im breadboard testing it, the arduino will run off its own supply and ill use a 9volt battery just for the motor, should I tie the battery ground to the arduino. My instinct would not to, but Ive heard someone saying about having to tie grounds when using transistors. Any one want to elaborate?