I'm sorry, I meant all
four IN lines. There are four IN pins on the IC (marked 1A, 2A, 3A, and 4A on the
datasheet), and two enable lines (1,2EN and 3,4EN).
When I refer to "IN" lines I mean the 1A, 2A, 3A, and 4A pins, and by "OUT" I mean 1Y, 2Y, 3Y, and 4Y. Enable pins refer to 1,2EN and 3,4EN.
The enable lines can/should be connected to PWM outputs on the Arduino, letting you use analogWrite() to set the duty cycle, while the four IN lines can be connected to any digital output on the Arduino. IN1A and IN2A control outputs 1Y and 2Y - if 1A is HIGH and 2A is LOW, and the motor is connected to 1Y and 2Y, the motor will run in one direction at a speed roughly proportional to the PWM duty cycle on 1,2EN. If you swap 1A and 2A such that 1A is LOW and 2A is HIGH, the motor will run at the same speed in the opposite direction.
In the schematic, 1A and 2A are connected to a single IO line, with a transistor inverting the signal such that 1A and 2A are always opposite. This behavior allows you to use fewer IO lines to control motors, at the cost of losing the ability to brake: when 1A and 2A are both HIGH or both LOW, the motor contacts are shorted and the back-EMF generated from the motor will act as a rudimentary brake. In order to do this, the Arduino must individually control the IN lines - thus why I say you should just connect all four of the IN lines to your Arduino.