What made you choose two 9V batteries in series? There are a number of problems with this:
1) Your motors are intended for use at 6 V. As the product page says:
You are running them at over 18 V, which is three times higher than their rated voltage and gives them a stall current of approximately 10 A.
2) You are using a driver with a peak current rating of 5 A, and the 10 A stall current of your motors significantly exceeds this. This problem will go away if you reduce your motor voltage to something closer to what your motors can actually handle, like 6 V.
3) 9 V batteries are generally not strong enough to drive motors. This is one of the bullet points in the Read Before You Post: General Advice for Getting Help thread that is at the top of every forum. 9V batteries cannot deliver much current, and their voltage falls dramatically when you try to draw more than they can supply. You should switch to a more appropriate power supply, like a 4-AA battery holder with alkaline cells or a 5-AA NiMH battery pack.
You don't need to do anything with the fault status (FS) pins to use the driver. These pins exist to give you feedback about the state of the driver so you can detect and potentially respond to faults. If you want to use them, you need to connect them as I (and the product page) describe, but it is fine to leave them disconnected. As the product page says: