Hello,
I'm new to arduino and electronics so sorry if this is a newbie question. I'm planning to power an arduino with 6xAA batteries (9V total through DC plug), and using the arduino's 5v output pin to power the L293D to control two motors. I know the L293D can handle 4-36V on pin 8, but pin 16 only handles 5V. Will it be okay to power the whole ic with just the arduino 5V pin, regardless of the amperage given by the 6xAA batteries?
No. It is a really bad idea to run motors from the Arduino 5V pin. It can't provide enough current even for very small motors.
What you need to do is to split your battery connection so it goes direct to the L293D pin 8. You can then connect the Arduino 5V pin to pin 16 on the L293D.
Steve
Indeed, power motors directly from the battery.
Note that your motors will only see about 7V, the rest is lost in this chip, which drops about 2V by itself. It's an ancient design after all...