On my motor driver there is only 2 pins output for Motor A and 2 pins output for Motor B. My stepper motor has 4 input pins so how do I connect this to my stepper motor??
So your question is: i have 2 pair of outputs, how do i connect them to my motor that has 4 wires ?
You can look up your motor's datasheet or use a multimeter to find out what wires belong together of that motor.
The datasheet will tell you how to wire it up.
Beeping the wires with your multimeter just tells you the pairs that belong together.
After beeping you might need to reverse polarity on one of the pairs to get them to work as expected or you need to write alternative code that handles this.
I can't think of a reason why it would not work if you connect your driver directly to the Arduino.
The use of JimboZA's L297 might make it easier to control the motor, and will probably save you some pins.