You do need diodes with the L293NE, see the datasheet (the L293D has them built in).
As jwatte says, to control a motor you need a pwm pin for speed and a simple digital pin for direction. So you need to use 4 of your 6 pwm pins. If you don't have 8 pins available in total, you could share some of the direction control pins between motors, if you don't need to control the direction of each motor independently of all the others.