I need to know how to use the 2N3906 transistor with a min. 6V motor. I also have an external battery and when I attach the motor without the Arduino it works fine. I am also using a Arduino Mega 2560
That transistor is limited to 200mA collector current and isn't suitable for driving a motor which typically take an amp or more in stall. Just how miniature is the motor (what is the winding resistance for instance).