I would clearly prefer the input over the enable...
From what I have seen in a scope, the enable lines some times have considerable rising times... Producing a oscilating something like signal...
The signal was far more predicted when PWM on the input, rather than enable...
Effective PWM signals for DC motos are somewhere near 10 - 15kHz... Personally even as high as 20 - 22kHz, which is good cause is beyond the human hearing range. This is something you should chooce depending on the inductance of the motor.
And depending on the inductance of the motor it's best to use a capacitor between the motor leads AND each lead and the motor casing, so that energy stored at the LC system, which could be of even 100V, can be driven elsewhere and not the H-bridge ;-)
I haven't really studied how all these methods are called, but there are actually some very nice tutorials out there....
Also... you are probably considering an IC and not power transistors or Mosfets right???