Powering an SN754410E from Arduino logic pins
Yes, the enable pins 1,9 going to an MCU port is correct. 

But the SN754410E is unsuitable for driving low voltage stepper motors because it cannot provide rail to rail switching.  

If you look at the datasheet:  

The output stage looks like this: 



The output voltage is limited as below:  

  

With a 5 V supply for your stepper motor you could only deliver about 1.4 V to the stepper motor windings. Surprisingly you might actually find this allowed you to step a small stepper motor without any load. 

To get 5 V supply for motor windings you'd need a supply minimum of about 8.6 V.
Now if you wanted to you could run your Arduino from 9 V and use that to supply both the Arduino and the Stepper drive supply, that would work. In that case you could connect the supply pins 8,16 together, making sure your supply is well decoupled.